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Leivar P.,University of California at Berkeley | Leivar P.,Plant Gene Expression Center | Leivar P.,Center for Research in Agricultural Genomics | Quail P.H.,University of California at Berkeley | Quail P.H.,Plant Gene Expression Center
Trends in Plant Science | Year: 2011

A small subset of basic helix-loop-helix transcription factors called PIFs (phytochrome-interacting factors) act to repress seed germination, promote seedling skotomorphogenesis and promote shade-avoidance through regulated expression of over a thousand genes. Light-activated phytochrome molecules directly reverse these activities by inducing rapid degradation of the PIF proteins. Here, we review recent advances in dissecting this signaling pathway and examine emerging evidence that indicates that other pathways also converge to regulate PIF activity, including the gibberellin pathway, the circadian clock and high temperature. Thus PIFs have broader roles than previously appreciated, functioning as a cellular signaling hub that integrates multiple signals to orchestrate regulation of the transcriptional network that drives multiple facets of downstream morphogenesis. The relative contributions of the individual PIFs to this spectrum of regulatory functions ranges from quantitatively redundant to qualitatively distinct. © 2010 Elsevier Ltd.

Giner A.,Center for Research in Agricultural Genomics
PLoS pathogens | Year: 2010

RNA silencing is an evolutionarily conserved sequence-specific gene-inactivation system that also functions as an antiviral mechanism in higher plants and insects. To overcome antiviral RNA silencing, viruses express silencing-suppressor proteins. These viral proteins can target one or more key points in the silencing machinery. Here we show that in Sweet potato mild mottle virus (SPMMV, type member of the Ipomovirus genus, family Potyviridae), the role of silencing suppressor is played by the P1 protein (the largest serine protease among all known potyvirids) despite the presence in its genome of an HC-Pro protein, which, in potyviruses, acts as the suppressor. Using in vivo studies we have demonstrated that SPMMV P1 inhibits si/miRNA-programmed RISC activity. Inhibition of RISC activity occurs by binding P1 to mature high molecular weight RISC, as we have shown by immunoprecipitation. Our results revealed that P1 targets Argonaute1 (AGO1), the catalytic unit of RISC, and that suppressor/binding activities are localized at the N-terminal half of P1. In this region three WG/GW motifs were found resembling the AGO-binding linear peptide motif conserved in metazoans and plants. Site-directed mutagenesis proved that these three motifs are absolutely required for both binding and suppression of AGO1 function. In contrast to other viral silencing suppressors analyzed so far P1 inhibits both existing and de novo formed AGO1 containing RISC complexes. Thus P1 represents a novel RNA silencing suppressor mechanism. The discovery of the molecular bases of P1 mediated silencing suppression may help to get better insight into the function and assembly of the poorly explored multiprotein containing RISC.

Vicient C.M.,Center for Research in Agricultural Genomics
BMC Genomics | Year: 2010

Background: Mobile genetic elements represent a high proportion of the Eukaryote genomes. In maize, 85% of genome is composed by transposable elements of several families. First step in transposable element life cycle is the synthesis of an RNA, but few is known about the regulation of transcription for most of the maize transposable element families. Maize is the plant from which more ESTs have been sequenced (more than two million) and the third species in total only after human and mice. This allowed us to analyze the transcriptional activity of the maize transposable elements based on EST databases.Results: We have investigated the transcriptional activity of 56 families of transposable elements in different maize organs based on the systematic search of more than two million expressed sequence tags. At least 1.5% maize ESTs show sequence similarity with transposable elements. According to these data, the patterns of expression of each transposable element family is variable, even within the same class of elements. In general, transcriptional activity of the gypsy-like retrotransposons is higher compared to other classes. Transcriptional activity of several transposable elements is specially high in shoot apical meristem and sperm cells. Sequence comparisons between genomic and transcribed sequences suggest that only a few copies are transcriptionally active.Conclusions: The use of powerful high-throughput sequencing methodologies allowed us to elucidate the extent and character of repetitive element transcription in maize cells. The finding that some families of transposable elements have a considerable transcriptional activity in some tissues suggests that, either transposition is more frequent than previously expected, or cells can control transposition at a post-transcriptional level. © 2010 Vicient; licensee BioMed Central Ltd.

Farinas B.,Center for Research in Agricultural Genomics | Mas P.,Center for Research in Agricultural Genomics
Plant Journal | Year: 2011

Despite our increasing understanding of the molecular determinants essential for circadian clock function, we still lack a complete picture of the mechanisms contributing to clock progression in plants. Here, we explore the role of REVEILLE8/LHY-CCA1-LIKE5 (RVE8/LCL5) within the Arabidopsis circadian system. RVE8/LCL5 encodes a MYB-like transcription factor similar to CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) and ELONGATED HYPOCOTYL (LHY), which are essential regulators of the Arabidopsis circadian clock. Consistent with the sequence similarity, the rhythmic expression of RVE8/LCL5 shows a morning acrophase comparable to that of CCA1 and LHY. Plants mis-expressing RVE8/LCL5 display a variety of circadian phenotypes, including altered circadian gene expression and photoperiodic flowering time. Similar to CCA1, RVE8/LCL5 regulates the expression of the oscillator gene TOC1 (TIMING OF CAB EXPRESSION1) by associating with the TOC1 promoter and by modulating the pattern of histone 3 (H3) acetylation. However, the mechanisms of RVE8/LCL5 and CCA1 activity in this regulation differ markedly. Indeed, the use of chromatin immunoprecipitation and pharmacological inhibition assays reveals that RVE8/LCL5 favours a hyper-acetylated state of H3 at the TOC1 promoter, which may facilitate the rising phase of TOC1. In contrast, CCA1 represses TOC1 expression by promoting histone deacetylation. Thus, despite the sequence homology and the similar morning phase of expression, RVE8/LCL5 and CCA1 have opposing regulatory functions within the Arabidopsis circadian clock, although CCA1 has a more predominant role. We propose that contrasting chromatin compaction and transcriptional modulation through the opposing activities of RVE8/LCL5 and CCA1 might provide a fine-tuning mechanism for precisely shaping the TOC1 circadian waveform in Arabidopsis. © 2011 Blackwell Publishing Ltd.

Rodriguez-Concepcion M.,Center for Research in Agricultural Genomics
Archives of Biochemistry and Biophysics | Year: 2010

Carotenoids are isoprenoids of industrial and nutritional interest produced by all photosynthetic organisms, including plants. Too often, the metabolic engineering of plant carotenogenesis has been obstructed by our limited knowledge on how the endogenous pathway interacts with other related metabolic pathways, particularly with those involved in the production of isoprenoid precursors. However, recent discoveries are providing new insights into this field. All isoprenoids derive from prenyl diphosphate precursors. In the case of carotenoids, these precursors are produced predominantly by the methylerythritol 4-phosphate (MEP) pathway in plants. This review focuses on the progress in our understanding of how manipulation of the MEP pathway impacts carotenoid biosynthesis and on the discoveries underlining the central importance of coordinating the supply of MEP-derived precursors with the biosynthesis of carotenoids and other derived isoprenoids. © 2010 Elsevier Inc.

Troncoso-Ponce M.A.,Center for Research in Agricultural Genomics | Mas P.,Center for Research in Agricultural Genomics
Molecular Plant | Year: 2012

The circadian clock temporally coordinates plant growth and metabolism in close synchronization with the diurnal and seasonal environmental changes. Research over the last decade has identified a number of clock components and a variety of regulatory mechanisms responsible for the rhythmic oscillations in metabolic and physiological activities. At the core of the clock, transcriptional/translational feedback loops modulate the expression of a significant proportion of the genome. In this article, we briefly describe some of the very recent advances that have improved our understanding of clock organization and function in Arabidopsis thaliana. The new studies illustrate the role of clock protein complex formation on circadian gating of plant growth and identify alternative splicing as a new regulatory mechanism for clock function. Examination of key clock properties such as temperature compensation has also opened new avenues for functional research within the plant clockwork. The emerging connections between the circadian clock and metabolism, hormone signaling and response to biotic and abiotic stress also add new layers of complexity to the clock network and underscore the significance of the circadian clock regulating the daily life of plants. © 2012 The Author.

Henriques R.,Rockefeller University | Mas P.,Center for Research in Agricultural Genomics
Seminars in Cell and Developmental Biology | Year: 2013

Circadian clocks are endogenous mechanisms that translate environmental cues into temporal information to generate the 24-h rhythms in metabolism and physiology. The circadian function relies on the precise regulation of rhythmic gene expression at the core of the oscillator, which temporally modulates the genome transcriptional activity in virtually all multicellular organisms examined to date. Emerging evidence in plants suggests a highly sophisticated interplay between the circadian patterns of gene expression and the rhythmic changes in chromatin remodeling and histone modifications. Alternative precursor messenger RNA (pre-mRNA) splicing has also been recently defined as a fundamental pillar within the circadian system, providing the required plasticity and specificity for fine-tuning the circadian clock. This review highlights the relationship between the plant circadian clock with both chromatin remodeling and alternative splicing and compares the similarities and divergences with analogous studies in animal circadian systems. © 2013 Elsevier Ltd.

Portoles S.,Center for Research in Agricultural Genomics | Mas P.,Center for Research in Agricultural Genomics
PLoS Genetics | Year: 2010

Circadian rhythms are daily biological oscillations driven by an endogenous mechanism known as circadian clock. The protein kinase CK2 is one of the few clock components that is evolutionary conserved among different taxonomic groups. CK2 regulates the stability and nuclear localization of essential clock proteins in mammals, fungi, and insects. Two CK2 regulatory subunits, CKB3 and CKB4, have been also linked with the Arabidopsis thaliana circadian system. However, the biological relevance and the precise mechanisms of CK2 function within the plant clockwork are not known. By using ChIP and Double-ChIP experiments together with in vivo luminescence assays at different temperatures, we were able to identify a temperature-dependent function for CK2 modulating circadian period length. Our study uncovers a previously unpredicted mechanism for CK2 antagonizing the key clock regulator CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1). CK2 activity does not alter protein accumulation or subcellular localization but interferes with CCA1 binding affinity to the promoters of the oscillator genes. High temperatures enhance the CCA1 binding activity, which is precisely counterbalanced by the CK2 opposing function. Altering this balance by over-expression, mutation, or pharmacological inhibition affects the temperature compensation profile, providing a mechanism by which plants regulate circadian period at changing temperatures. Therefore, our study establishes a new model demonstrating that two opposing and temperature-dependent activities (CCA1-CK2) are essential for clock temperature compensation in Arabidopsis. © 2010 Portolé s, Más.

Coca M.,Center for Research in Agricultural Genomics | San Segundo B.,Center for Research in Agricultural Genomics
Plant Journal | Year: 2010

In mammals, lipid bodies play a key role during pathological and infectious diseases. However, our knowledge on the function of plant lipid bodies, apart from their role as the major site of lipid storage in seed tissues, remains limited. Here, we provide evidence that a calcium-dependent protein kinase (CPK) mediates pathogen resistance in Arabidopsis. AtCPK1 expression is rapidly induced by fungal elicitors. Loss-of-function mutants of AtCPK1 exhibit higher susceptibility to pathogen infection compared to wild-type plants. Conversely, over-expression of AtCPK1 leads to accumulation of salicylic acid (SA) and constitutive expression of SA-regulated defence and disease resistance genes, which, in turn, results in broad-spectrum protection against pathogen infection. Expression studies in mutants affected in SA-mediated defence responses revealed an interlocked feedback loop governing AtCPK1 expression and components of the SA-dependent signalling pathway. Moreover, we demonstrate the dual localization of AtCPK1 in lipid bodies and peroxisomes. Overall, our findings identify AtCPK1 as a component of the innate immune system of Arabidopsis plants. © 2010 Blackwell Publishing Ltd.

Suarez-Lopez P.,Center for Research in Agricultural Genomics
Frontiers in Plant Science | Year: 2013

The identification of FLOWERING LOCUS T (FT) and several FT homologs as phloem-mobile proteins that regulate flowering has sparked the search for additional homologs involved in the long-distance regulation of other developmental processes. Given that flowering and tuber induction share regulatory pathways, the quest for long-distance tuberization signals has been further stimulated. Several tuberization regulators have been proposed as mobile molecules, including the FT family protein StSP6A, the plant growth regulators gibberellins and the microRNA miR172. Although some of these hypotheses are attractive and plausible, evidence that these molecules are transmissible in potato has yet to be obtained. Two mRNAs encoding transcription factors, StBEL5 and POTATO HOMEOBOX 1 (POTH1), are mobile and correlate with tuber induction. However, evidence that StBEL5 or POTH1 are required for tuberization is not available yet. Therefore, there are several good candidates for long-distance molecules in the tuberization process. Further research should test their role as systemic tuberization signals. © 2013 Suárez-López.

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