Plant development meets cell proliferation in Madrid

Immunity and the Animation of the Genome

Expression of genes in the right place at the right time is fundamental to all of life. The ontogeny of effector and memory T cells is a robust example of this important principle. Although lymphocytes represent a late addition in animal evolution, they are serving as an exceptional model system to unlock the mysteries surrounding the way in which the genome is animated. It will be speculated here that further insight into fundamental principles of genome function may arise from study of immunity. Likewise, such information may be key to understanding and altering immunobiology.

A genome-wide identification of E2F-regulated genes in Arabidopsis

The completion of the Arabidopsis genomic sequence offers the possibility to extract global information about regulatory mechanisms. Here, we describe a data mining strategy in combination with gene expression analysis to identify bona fide genes regulated by the E2F transcription factor. Starting with a genome-wide search of chromosomal sites containing E2F-binding sites, we studied in depth two of the most abundant E2F-binding sites within the Arabidopsis genome and identified over 180 potential E2F target genes. Among them and in addition to cell cycle-related genes, we have also identified genes belonging to other functional categories, e.g. transcription, stress and defense or signaling. We have determined the expression levels of genes selected from different categories under two experimental situations. Using cultured cells partially synchronized with aphidicolin, we found that most potential E2F targets identified in silico show a cell cycle-regulated expression pattern with a peak in early/mid S-phase. In addition, we used Arabidopsis transgenic plants expressing a DP gene containing a truncated DNA-binding domain, which likely has a dominant-negative effect on AtE2Fa, b and c (also named AtE2F3, 1 and 2, respectively), which require DP for efficient DNA binding. Contrary to the up-regulation observed in early/mid S-phase-cultured cells, the expression of a large number of potential E2F targets was decreased in the transgenic plants. Our results strongly support that the RBR/E2F pathway plays a crucial role in regulating the expression of the genes identified in this study.

G(1) to S transition: more than a cell cycle engine switch

CDK-cyclin complexes are the universal drivers of cell cycle transitions. Progression through G(1) and transition to S-phase, thereby initiating genome duplication, requires the concerted action of cyclin-dependent kinase (CDK)-cyclin complexes on specific targets. These targets belong to at least two major regulatory networks: the retinoblastoma-related (RBR)/E2F pathway and complexes that are responsible for the initiation of DNA replication. The G(1) phase is central to the integration of signals that regulate both the exit from the cell division cycle to differentiation and the reactivation of cell proliferation. Cellular factors that are involved in these pathways play a role in regulating cell size and number, and organogenesis. As a consequence, they are also involved in determining plant architecture.

Interleukin-1 beta-mediated suppression of RXR:RAR transactivation of the Ntcp promoter is JNK-dependent

Bile flow is rapidly and markedly reduced in hepatic inflammation, correlating with suppression of critical hepatic bile acid transporter gene expression, including the principal hepatic bile acid importer, the Na(+)/taurocholate co-transporting polypeptide (Ntcp, Slc10a1). Endotoxin treatment of rats and interleukin-1 beta (IL-1 beta) treatment of liver-derived HepG2 cells leads to a marked decline in the nuclear binding activity of a main Ntcp gene regulator, the nuclear receptor heterodimer retinoid X receptor:retinoic acid receptor (RXR:RAR). How IL-1 beta signaling leads to reduced RXR:RAR nuclear binding activity is unknown, and we sought to determine whether mitogen-activated protein kinase (MAPK) pathways were involved. IL-1 beta treatment of cultured primary rat hepatocytes markedly reduced Ntcp RNA levels and Ntcp promoter activity in transiently transfected HepG2 cells. Pretreatment with inhibitors of extracellular signal-regulated kinase (ERK, PD98059) or p38 MAPK (SB203580) did not affect IL-1 beta-mediated suppression of Ntcp gene expression, whereas curcumin, a derivative of the spice turmeric and a recently described inhibitor of c-Jun N-terminal kinase (JNK), completely ameliorated the effects of IL-1 beta. Co-transfection of a JNK expression plasmid inhibited RXR:RAR-mediated activation of the Ntcp promoter, while a dominant negative JNK expression plasmid completely blocked IL-1 beta-mediated suppression. Curcumin, but not PD98059 or SB203580, inhibited IL-1 beta-mediated suppression of nuclear RXR:RAR binding activity, which correlated with inhibition of JNK phosphorylation and phospho-JNK-mediated phosphorylation of RXR. Taken together, these data provide evidence supporting a novel player (JNK), as well as its inhibitor (curcumin), in inflammation-mediated regulation of hepatobiliary transporters and correlate JNK-dependent RXR phosphorylation with reduced RXR-dependent hepatic gene expression.