Signal-specific Manner Research Articles

An array of signal-specific MoYpd1 isoforms determines full virulence in the pathogenic fungus Magnaporthe oryzae

Magnaporthe oryzae is placed first on a list of the world’s top ten plant pathogens with the highest scientific and economic importance. The locus MGG_07173 occurs only once in the genome of M. oryzae and encodes the phosphotransfer protein MoYpd1p, which plays an important role in the high osmolarity glycerol (HOG) signaling pathway for osmoregulation. Originating from this locus, at least three MoYPD1 isoforms are produced in a signal-specific manner. The transcript levels of these MoYPD1-isoforms were individually affected by external stress. Salt (KCI) stress raised MoYPD1_T0 abundance, whereas osmotic stress by sorbitol elevates MoYPD1_T1 levels. In line with this, signal-specific nuclear translocation of green fluorescent protein-fused MoYpd1p isoforms in response to stress was observed. Mutant strains that produce only one of the MoYpd1p isoforms are less virulent, suggesting a combination thereof is required to invade the host successfully. In summary, we demonstrate signal-specific production of MoYpd1p isoforms that individually increase signal diversity and orchestrate virulence in M. oryzae.

The Role of the Proteasome in Platelet Function.

Platelets are megakaryocyte-derived acellular fragments prepped to maintain primary hemostasis and thrombosis by preserving vascular integrity. Although they lack nuclei, platelets harbor functional genomic mediators that bolster platelet activity in a signal-specific manner by performing limited de novo protein synthesis. Furthermore, despite their limited protein synthesis, platelets are equipped with multiple protein degradation mechanisms, such as the proteasome. In nucleated cells, the functions of the proteasome are well established and primarily include proteostasis among a myriad of other signaling processes. However, the role of proteasome-mediated protein degradation in platelets remains elusive. In this review article, we recapitulate the developing literature on the functions of the proteasome in platelets, discussing its emerging regulatory role in platelet viability and function and highlighting how its functional coupling with the transcription factor NF-κB constitutes a novel potential therapeutic target in atherothrombotic diseases.

RNA polymerase II pausing can be retained or acquired during activation of genes involved in the epithelial to mesenchymal transition.

Promoter-proximal RNA polymerase II (Pol II) pausing is implicated in the regulation of gene transcription. However, the mechanisms of pausing including its dynamics during transcriptional responses remain to be fully understood. We performed global analysis of short capped RNAs and Pol II Chromatin Immunoprecipitation sequencing in MCF-7 breast cancer cells to map Pol II pausing across the genome, and used permanganate footprinting to specifically follow pausing during transcriptional activation of several genes involved in the epithelial to mesenchymal transition (EMT). We find that the gene for EMT master regulator Snail (SNAI1), but not Slug (SNAI2), shows evidence of Pol II pausing before activation. Transcriptional activation of the paused SNAI1 gene is accompanied by a further increase in Pol II pausing signal, whereas activation of non-paused SNAI2 gene results in the acquisition of a typical pausing signature. The increase in pausing signal reflects increased transcription initiation without changes in Pol II pausing. Activation of the heat shock HSP70 gene involves pausing release that speeds up Pol II turnover, but does not change pausing location. We suggest that Pol II pausing is retained during transcriptional activation and can further undergo regulated release in a signal-specific manner.

Dynamic Visualization of mTORC1 Activity in Living Cells

The mechanistic target of rapamycin complex 1 (mTORC1) senses diverse signals to regulate cell growth and metabolism. It has become increasingly clear that mTORC1 activity is regulated in time andspace inside the cell, but direct interrogation ofsuch spatiotemporal regulation is challenging. Here, we describe a genetically encoded mTORC1 activity reporter (TORCAR) that exhibits a change in FRET in response to phosphorylation by mTORC1. Co-imaging mTORC1 activity and calcium dynamics revealed that a growth-factor-induced calcium transient contributes to mTORC1 activity. Dynamic activity maps generated with the use of subcellularly targeted TORCAR uncovered mTORC1 activity not only in cytosol and at the lysosome but also in the nucleus and at the plasma membrane. Furthermore, a wide distribution of activities was observed upon growth factor stimulation, whereas leucine ester, an amino acid surrogate, induces more compartmentalized activities at the lysosome and in the nucleus. Thus, mTORC1 activities are spatiotemporally regulated in a signal-specific manner.

Regulation of Primary Response Genes in B Cells

Deregulated gene expression in B cells often results in various lymphoid malignancies and immune deficiencies. Therefore, understanding signal-induced gene regulatory pathways involved during B cell activation is important to tackle pathologies associated with altered B cell function. Primary response genes (PRGs) are rapidly induced upon signaling in B cells and other cell types and often encode oncogenic transcription factors, which are associated with various malignancies. However, an important issue that remains unclear is whether the fundamental mechanism of activation of these genes is essentially the same under such diverse conditions. c-fos is a PRG that is induced rapidly upon activation of B cells in response to a wide variety of stimuli. Using the c-fos gene as a candidate PRG, we addressed here how it is regulated in response to tumor-promoting and antigen-mimicking signals. Our results show that although the mRNA was induced and extinguished within minutes in response to both signals, surprisingly, apparently full-length unspliced pre-mRNA persisted for several hours in both cases. However, although the mitogenic signal resulted in a more sustained mRNA response that persisted for 4 h, antigenic signaling resulted in a more robust but very transient response that lasted for <1 h. Moreover, the pre-mRNA profile exhibited significant differences between the two signals. Additionally, the splicing regulation was also observed with egr-2, but not with c-myc. Together, these results suggest a previously underappreciated regulatory step in PRG expression in B cells.

SIMPL Enhancement of Tumor Necrosis Factor-α Dependent p65-MED1 Complex Formation Is Required for Mammalian Hematopoietic Stem and Progenitor Cell Function

Significant insight into the signaling pathways leading to activation of the Rel transcription factor family, collectively termed NF-κB, has been gained. Less well understood is how subsets of NF-κB-dependent genes are regulated in a signal specific manner. The SIMPL protein (signaling molecule that interacts with mouse pelle-like kinase) is required for full Tumor Necrosis Factor-α (TNFα) induced NF-κB activity. We show that SIMPL is required for steady-state hematopoiesis and the expression of a subset of TNFα induced genes whose products regulate hematopoietic cell activity. To gain insight into the mechanism through which SIMPL modulates gene expression we focused on the Tnf gene, an immune response regulator required for steady-state hematopoiesis. In response to TNFα SIMPL localizes to the Tnf gene promoter where it modulates the initiation of Tnf gene transcription. SIMPL binding partners identified by mass spectrometry include proteins involved in transcription and the interaction between SIMPL and MED1 was characterized in more detail. In response to TNFα, SIMPL is found in p65-MED1 complexes where SIMPL enhances p65/MED1/SIMPL complex formation. Together our results indicate that SIMPL functions as a TNFα-dependent p65 co-activator by facilitating the recruitment of MED1 to p65 containing transcriptional complexes to control the expression of a subset of TNFα-induced genes.

Bim: Guardian of Tissue Homeostasis and Critical Regulator of the Immune System, Tumorigenesis and Bone Biology

One of the most important roles of apoptosis is the maintenance of tissue homeostasis. Impairment of apoptosis leads to a number of pathological conditions. In response to apoptotic signals, various proteins are activated in a pathway and signal-specific manner. Recently, the pro-apoptotic molecule Bim has attracted increasing attention as a pivotal regulator of tissue homeostasis. The Bim expression level is strictly controlled in both transcriptional and post-transcriptional levels. This control is dependent on cell, tissue and apoptotic stimuli. The phenotype of Bim-deficient mice is a systemic lupus erythematosus-like autoimmune disease with an abnormal accumulation of hematopoietic cells. Bim is thus a critical regulator of hematopoietic cells and immune system. Further studies have revealed the critical roles of Bim in various normal and pathological conditions, including bone homeostasis and tumorigenesis. The current understanding of Bim signaling and roles in the maintenance of tissue homeostasis is reviewed in this paper, focusing on the immune system, bone biology and tumorigenesis to illustrate the diversified role of Bim.

Stress induced gene expression: a direct role for MAPKAP kinases in transcriptional activation of immediate early genes

Immediate early gene (IEG) expression is coordinated by multiple MAP kinase signaling pathways in a signal specific manner. Stress-activated p38α MAP kinase is implicated in transcriptional regulation of IEGs via MSK-mediated CREB phosphorylation. The protein kinases downstream to p38, MAPKAP kinase (MK) 2 and MK3 have been identified to regulate gene expression at the posttranscriptional levels of mRNA stability and translation. Here, we analyzed stress-induced IEG expression in MK2/3-deficient cells. Ablation of MKs causes a decrease of p38α level and p38-dependent IEG expression. Unexpectedly, restoration of p38α does not rescue the full-range IEG response. Instead, the catalytic activity of MKs is necessary for the major transcriptional activation of IEGs. By transcriptomics, we identified MK2-regulated genes and recognized the serum response element (SRE) as a common promoter element. We show that stress-induced phosphorylation of serum response factor (SRF) at serine residue 103 is significantly reduced and that induction of SRE-dependent reporter activity is impaired and can only be rescued by catalytically active MK2 in MK2/3-deficient cells. Hence, a new function of MKs in transcriptional activation of IEGs via the p38α-MK2/3-SRF-axis is proposed which probably cooperates with MKs’ role in posttranscriptional gene expression in inflammation and stress response.

Transcriptional mediator subunit Med1 is required for the expression of metastasis‐associated gene, The death associated protein kinase‐1 (DAPK1)

The death associated protein kinase‐1 (DAPK1) is a ca+2/calmodulin regulated serine/threonine kinase and is a major tumor suppressor gene. Its expression is lost in multiple tumor types although the mechanisms are unclear. Recently we showed that both the basal and IFN‐γ induced dapk1 expression levels were critically dependent on transcription factor C/EBP‐β (P.Gade et al (2008) Mol. Cell. Biol.), which plays major role in regulating energy metabolism, immune response and cell differentiation. C/EBP‐β associates with various cellular factors to exert its activity in gene context and signal specific manner. We have recently reported that Med1 subunit of the transcriptional mediator complex specifically interacts with C/EBP‐β for stimulating dapk1 expression in an IFN‐induced manner. We investigated if the mechanism responsible for the loss of dapk1 expression in human cancers involves a failure to recruit C/EBP‐β and Med1 to the dapk1 promoter. We found a significantly lower occupancy of Med1 and C/EBP‐β at dapk1 promoter in human cancer cell lines compared to the normal control cells. More importantly, the loss of Med1 expression correlated with a corresponding loss of dapk1 expression in a number of primary human lung carcinomas. Restoration of Med1 into cancer cells not only induced the expression of dapk1 but also suppressed their metastatic potential in vivo. Thus, our studies identified Med1 as one critical parameter that limits dapk1 expression in human cancers.

BAD: undertaker by night, candyman by day

The BH3-only pro-apoptotic proteins are upstream sensors of cellular damage that selectively respond to specific, proximal death and survival signals. Genetic models and biochemical studies indicate that these molecules are latent killers until activated through transcriptional or post-translational mechanisms in a tissue-restricted and signal-specific manner. The large number of BH3-only proteins, their unique subcellular localization, protein-interaction network and diverse modes of activation suggest specialization of their damage-sensing function, ensuring that the core apoptotic machinery is poised to receive input from a wide range of cellular stress signals. The apoptotic response initiated by the activation of BH3-only proteins ultimately culminates in allosteric activation of pro-apoptotic BAX and BAK, the gateway proteins to the mitochondrial pathway of apoptosis. From activation of BH3-only proteins to oligomerization of BAX and BAK and mitochondrial outer membrane permeabilization, an intricate network of interactions between the pro- and anti-apoptotic members of the BCL-2 family orchestrates the decision to undergo apoptosis. Beyond regulation of apoptosis, multiple BCL-2 proteins have recently emerged as active components of select homeostatic pathways carrying other cellular functions. This review focuses on BAD, which was the first BH3-only protein linked to proximal survival signals through phosphorylation by survival kinases. In addition to findings that delineated the physiological role of BAD in apoptosis and its dynamic regulation by phosphorylation, studies pointing to new roles for this protein in other physiological pathways, such as glucose metabolism, are highlighted. By executing its 'day' and 'night' jobs in metabolism and apoptosis, respectively, BAD helps coordinate mitochondrial fuel metabolism and the apoptotic machinery.

Regulation of root‐wave response by extra large and conventional G proteins in Arabidopsis thaliana

Heterotrimeric G proteins composed of alpha, beta and gamma subunits regulate a number of fundamental processes concerned with growth and development in plants. In addition to the canonical heterotrimeric G proteins, plants also contain a small family of extra large G proteins (XLGs) that show significant similarity to the G-protein alpha subunit in their C-terminal regions. In this paper we show that one of the three XLG genes, XLG3, and the Gbeta subunit (AGB1) of the Arabidopsis G-protein heterotrimer are specifically involved in the regulation of a subset of root morphological and growth responses. Based on analysis of T-DNA insertional mutant phenotypes, XLG3 and AGB1 each positively regulate root waving and root skewing. Since these responses are regulated by physical as well as physiological cues, we assessed the roles of AGB1 and XLG3 in gravitropism, thigmotropism and hormonal responses. Our data show that mutants lacking either XLG3 or AGB1 genes are hypersensitive to ethylene and show growth responses consistent with alterations in auxin transport, while maintaining an essentially wild-type response to the physical cues of gravity and touch. These results suggest that XLG3 and AGB1 proteins regulate the hormonal determinants of root-waving and root-skewing responses in plants and possibly interact in a tissue-specific or signal-specific manner. Because plants harboring knockout mutations in the Galpha subunit gene, GPA1, exhibit wild-type root waving and skewing, our results may indicate that the AGB1 subunit functions in these processes without formation of a classic Galphabetagamma heterotrimer.

PDGF- and Insulin/IGF-1–Specific Distinct Modes of Class IAPI 3-Kinase Activation in Normal Rat Retinas and RGC-5 Retinal Ganglion Cells

To compare PDGF- and insulin/IGF-1-induced class I(A) PI 3-kinase/Akt survival signaling in normal retinas and retinal ganglion cells (RGCs). Normal rat retinas and RGC-5 cells were used for (1) immunohistochemical and immunoblot studies to detect PDGF receptor (PDGFR) subtypes and (2) immunoprecipitation, immunoblot, and in vitro lipid kinase assays to determine basal and PDGF-induced class I(A) PI 3-kinase/Akt survival signaling, in comparison with insulin or IGF-1 responses. Furthermore, RGC-5 cells were exposed to broad-spectrum (LY294002) or p110 isoform-selective (PI-103) PI 3-kinase inhibitors (versus Akt inhibitor) to assess the consequent effects on Akt phosphorylation, caspase-3/PARP cleavage, apoptotic phenotype, and cell viability, as a function of serum trophic factors. PDGFR-alpha and -beta immunoreactivity was observed in rat retinal Müller cells and in the RGC layer and blood vessels, respectively. In addition, PDGFR-alpha and -beta protein expression was observed in RGC-5 cells. Both retinas and RGC-5 cells exhibited a similar pattern of subunit-specific basal class I(A) PI 3-kinase activity, which was stimulated in a temporal and signal-specific manner by PDGF and insulin/IGF-1. Furthermore, RGC-5 cells showed PDGFR-alpha/beta tyrosine phosphorylation that induced the p85alpha regulatory subunit to activate p110alpha/beta-associated class I(A) PI 3-kinase, which in turn enhanced Akt phosphorylation. Exposure of serum-deprived RGC-5 cells to PI 3-kinase or Akt inhibitors increased susceptibility to apoptotic phenotype as revealed by caspase-3 and PARP cleavage. The present findings provide direct evidence of two distinct modes of retinal class I(A) PI 3-kinase activation that occurs in response to PDGF receptor and insulin/IGF-1 receptor stimulation. PDGF-induced PI 3-kinase/PIP3/Akt axis may provide new therapeutic approaches to ameliorate cell death in diabetic retinopathy and other retinal neurodegenerations.

The transcriptional coactivator and acetyltransferase p300 in fibroblast biology and fibrosis

The transcriptional coactivator p300 is a ubiquitous nuclear phosphoprotein and transcriptional cofactor with intrinsic acetyltransferase activity. p300 controls the expression of numerous genes in cell-type and signal-specific manner, and plays a pivotal role in cellular proliferation, apoptosis, and embryogenesis. By catalyzing acetylation of histones and transcription factors, p300 plays a significant role in epigenetic regulation. Recent evidence suggests that abnormal p300 function is associated with deregulated target gene expression, and is implicated in inflammation, cancer, cardiac hypertrophy, and genetic disorders such as the Rubinstein-Taybi syndrome. The activity of p300 is regulated at multiple levels, including developmental stage-specific expression, post-translational modifications, subcellular localization, and cell-type and gene-specific interactions with transcription factors. Although p300 has been investigated extensively in epithelial and hematopoietic cells, its role in fibroblast biology and tissue repair has received little attention to date. Recent studies implicate p300 in the regulation of collagen synthesis by transforming growth factor-beta (TGF-beta). Both the acetyltransferase activity of p300 and its inducible interaction with Smad3 are essential for mediating TGF-beta-induced stimulation of collagen synthesis. As a signal integrator whose availability for intracellular interactions with transcription factors is strictly limiting, p300 mediates the antagonistic regulation of TGF-beta-induced collagen synthesis by IFN-gamma and TNF-alpha via intracellular competition for limiting amount of p300. Significantly, p300 is itself a direct transcriptional target of TGF-beta in normal fibroblasts, and its levels are significantly elevated in fibrotic lesions as well as in experimental models of fibrosis. The emerging appreciation of the importance of p300 in extracellular matrix (ECM) remodeling and fibrosis and novel insights concerning the regulation, mechanism of action, and significance of p300 in fibroblast biology are discussed in this minireview.

From antigen to activation: specific signal transduction pathways linking antigen receptors to NF-κB

A precise balance between cellular apoptosis and cellular survival is essential for the proper functioning of the immune system. Whereas apoptosis eliminates self-reactive or supernumerary lymphocytes, survival signaling that counteracts apoptotic programs is needed to allow B and T lymphocytes that recognize pathogens to become activated and expand in response to infection. A major regulator of lymphocyte survival and activation is the transcription factor NF-κB. Controlled activation of NF-κB is essential for normal innate and adaptive immune responses, and dysregulated NF-κB signaling in lymphocytes contributes to diseases ranging from chronic inflammation and autoimmunity to lymphoma. The core NF-κB activating machinery composed of the NF-κB, IκB and IKK proteins is relatively well-characterized, but it is less clear how distinct upstream stimuli activate NF-κB in a tissue-, time- and signal-specific manner. In this review, we discuss recent insights into the specific signal transduction pathways leading to NF-κB activation that are triggered by engagement of the antigen receptors of T and B cells. We focus mainly on T cell receptor (TCR)-mediated NF-κB activation and draw parallels to B cell receptor (BCR)-mediated NF-κB activation where appropriate.

Differential effects of JNK1 and JNK2 on signal specific induction of apoptosis.

The c-Jun N-terminal kinases (JNKs) are activated by a variety of stress inducing agents and are thought to regulate apoptosis in a cell type and signal-specific manner. We have used fibroblasts lacking JNK1 or JNK2 to define their roles in response to different stress signals. Lack of JNK1 results in reduced c-Jun phosphorylation and resistance to UV-induced cell death. JNK2 deficient cells show increased sensitivity to UV irradiation which correlates with elevated and sustained phosphorylation of JNK1 and c-Jun. On the contrary, both Jnk1-/- and Jnk2-/- cells were more sensitive to tumor necrosis factor - alpha (TNF-alpha) and sorbitol-induced cell death. Treatment of Jnk1-/- cells with these reagents resulted in reduced JNK activity and a concomitant reduction of c-Jun phosphorylation, suggesting that phosphorylation of c-Jun does not influence TNF-alpha and sorbitol-induced apoptosis in fibroblasts. Moreover, both JNK1 and JNK2 appear to negatively regulate apoptosis independent of c-Jun phosphorylation. These data provide genetic evidence that although the JNK pathway is activated by a plethora of signals, it is required only for the induction of UV-induced cell death in a c-Jun phosphorylation-dependent manner, but not for TNF-alpha and sorbitol-induced apoptosis.

The Nedd4-like Protein KIAA0439 Is a Potential Regulator of the Epithelial Sodium Channel

The amiloride-sensitive epithelial sodium channel (ENaC) plays a critical role in fluid and electrolyte homeostasis and consists of alpha, beta, and gamma subunits. The carboxyl terminus of each ENaC subunit contains a PPxY, motif which is believed to be important for interaction with the WW domains of the ubiquitin-protein ligase, Nedd4. Disruption of this interaction, as in Liddle's syndrome, where mutations delete or alter the PPxY motif of either the beta or gamma subunits, has been proposed to result in increased ENaC activity. Here we present evidence that KIAA0439 protein, a close relative of Nedd4, is also a potential regulator of ENaC. We demonstrate that KIAA0439 WW domains bind all three ENaC subunits. We show that a recombinant KIAA0439 WW domain protein acts as a dominant negative mutant that can interfere with the Na(+)-dependent feedback inhibition of ENaC in whole-cell patch clamp experiments. We propose that KIAA0439 and Nedd4 proteins either play a redundant role in ENaC regulation or function in a tissue- and/or signal-specific manner to down-regulate ENaC.

Repression of Transcription by HoxC11 upon Phorbol Ester Stimulation

Hox genes encode transcription factors with a conserved DNA-binding domain and exhibit similar DNA-binding preferences. The in vivo specificity required for their biological function is brought about by combinatorial interactions with other factors. Such interactions also modulate their activation state. Here we show that HoxC11 can either activate or repress transcription in a signal-specific manner. We report the isolation of HoxC11 in a yeast one-hybrid screen for factors binding to a phorbol-ester, 12-O-tetradecanoylphorbol-13-acetate (TPA) response element (VLTRE), which is also a target for TPA-induced binding of Rel factors in gel-shift experiments. Although we detect no binding of in vitro translated HoxC11 to the TPA response element in EMSA, overexpression of HoxC11 in the HepG2 cell line leads to a complete block of TPA-induced transcription from a VLTRE-luciferase reporter. There is, however, no repression of the basal levels. The repression is furthermore not dependent on homeo-domain DNA binding. Our data suggest an interaction of HoxC11 with the basal-transcription machinery. We propose that HoxC11 is capable of mediating transcriptional activation or repression in a signal-specific manner and that its activation of the DNA target sequence in yeast might reflect in vivo recruitment to the promoter complex.

Modulation of human alpha1(I) procollagen gene activity by interaction with Sp1 and Sp3 transcription factors in vitro.

In previous work, we delineated a proximal region of the human alpha1(I) collagen gene (COL1A1) promoter necessary to direct its basal transcription in fibroblasts. This region has potential recognition sites for a variety of DNA-binding proteins. Here, we show that the -129/-107-bp sequence in this region of the promoter, which harbors an inverted CCAAT motif closely linked to a GC-rich direct repeat and is perfectly conserved between mouse and human, specifically bound the transcription factors Sp1, Sp3, and CTF/NF-1 in nuclear extracts from human skin and lung fibroblasts. Drosophila Schneider L2 cells lacking endogenous Sp activity were used to investigate the effect of expression of Sp or CTF/NF-1 transcription factors on COLlAl promoter activity. Expression of Sp1 caused potent trans-activation of a COL1A1 promoter (-174 to +42bp). In contrast, expression of Sp3, which binds to the same recognition sites as Sp1, and CTF/NF-1 stimulated COL1A1 promoter activity only at higher concentrations, and Sp2 did not transactivate. Expression of a 10-fold excess of Sp3, but not CTF/NF-1 or Sp2, abrogated the stimulation of COL1A1 promoter activity induced by Sp1. TGF-beta at concentrations previously shown to increase COL1A1 transcription caused a decrease in the relative amount of Sp3 in fibroblast nuclear extracts. These results suggest that both Sp1 and Sp3 bind to the proximal COL1A1 promoter and stimulate its activity; however, their interaction with each other may result in repression of Sp1-induced COL1A1 transcription. Alterations in the relative amounts or DNA-binding activities of these transcription factors in a cell- or signal-specific manner may contribute to the control of transcription from the COL1A1 promoter. The present findings, and recent observations implicating Sp1 and its homologs in regulating the expression of several collagen genes, suggest that the family of Sp1 transcription factors play a role in physiological and pathological modulation of connective tissue accumulation.