Phylogeny of the order Phyllachorales (Ascomycota, Sordariomycetes): among and within order relationships based on five molecular loci.

The order Phyllachorales (Pezizomycotina, Ascomycota) is a group of biotrophic, obligate plant parasitic fungi with a tropical distribution and high host specificity. Traditionally two families are recognised within this order: Phyllachoraceae and Phaeochoraceae, based mostly on morphological and host characteristics. Currently, the position of the order within the class Sordariomycetes is inconclusive, as well as the monophyly of the order, and its internal phylogenetic structure. Here we present a phylogeny of the order Phyllachorales based on sequence data of 29 species with a broad host range resulting from a wide geographical sampling. We inferred Maximum Likelihood and Bayesian phylogenies from data of five DNA regions: nrLSU rDNA, nrSSU rDNA, ITS rDNA, and the protein coding genes RPB2, and TEF1. We found that the order Phyllachorales is monophyletic and related to members of the subclass Sordariomycetidae within Sordariomycetes. Within the order, members of the family Phaeochoraceae form a monophyletic group, and the family Phyllachoraceae is split into two lineages. Maximum Likelihood ancestral state reconstructions indicate that the ancestor of Phyllachorales had a monocotyledonous host plant, immersed perithecia, and a black stroma. Alternative states of these characters evolved multiple times independently within the order. Based on our results we redefine the family Phyllachoraceae and propose the new family Telimenaceae with Telimena erythrinae as type species, resulting in three families in the order. Species of Telimena spp. occur in several monocotyledonous and eudicotyledonous host plants except Poaceae, and generally have enlarged black pseudostroma around the perithecia, a character not present in species of Phyllachoraceae.

Cofactor requirements for nuclear export of Rev response element (RRE)- and constitutive transport element (CTE)-containing retroviral RNAs. An unexpected role for actin.

Nuclear export of proteins containing leucine-rich nuclear export signals (NESs) is mediated by the export receptor CRM1/exportin1. However, additional protein factors interacting with leucine-rich NESs have been described. Here, we investigate human immunodeficiency virus type 1 (HIV-1) Rev-mediated nuclear export and Mason-Pfizer monkey virus (MPMV) constitutive transport element (CTE)-mediated nuclear export in microinjected Xenopus laevis oocytes. We show that eukaryotic initiation factor 5A (eIF-5A) is essential for Rev and Rev-mediated viral RNA export, but not for nuclear export of CTE RNA. In vitro binding studies demonstrate that eIF-5A is required for efficient interaction of Rev-NES with CRM1/exportin1 and that eIF-5A interacts with the nucleoporins CAN/nup214, nup153, nup98, and nup62. Quite unexpectedly, nuclear actin was also identified as an eIF-5A binding protein. We show that actin is associated with the nucleoplasmic filaments of nuclear pore complexes and is critically involved in export processes. Finally, actin- and energy-dependent nuclear export of HIV-1 Rev is reconstituted by using a novel in vitro egg extract system. In summary, our data provide evidence that actin plays an important functional role in nuclear export not only of retroviral RNAs but also of host proteins such as protein kinase inhibitor (PKI).

Regulation of acetylcholine receptor gene expression in human myasthenia gravis muscles. Evidences for a compensatory mechanism triggered by receptor loss.

Myasthenia gravis (MG) is a neuromuscular disorder mediated by antibodies directed against the acetylcholine receptor (nAChR) resulting in a functional nAChR loss. To analyze the molecular mechanisms involved at the muscular target site, we studied the expression of nAChR subunits in muscle biopsy specimens from MG patients. By using quantitative PCR with an internal standard for each subunit, we found that the levels of beta-, delta-, and epsilon-subunit mRNA coding for the adult nAChR were increased in severely affected MG patients, matching our previous data on the alpha-subunit. Messenger levels were highly variable in MG patients but not in controls, pointing to individual factors involved in the regulation of nAChR genes. The fetal subunit (gamma-chain) transcripts were almost undetectable in the extrajunctional region of MG muscle, suggesting that gene regulation in MG differs from that in the denervation model, in which nAChR gamma-subunit mRNA is reexpressed. Nicotinic AChR loss mediated by monoclonal anti-nAChR antibodies in both the TE671 muscle cell line and cultured normal human myotubes induces a similar increase in beta- alphand delta-subunit mRNA levels, suggesting the existence of a new muscular signaling pathway system coupled to nAChR internalization and independent of muscle electrical activity. These data demonstrate the existence of a compensatory mechanism regulating the expression of the genes coding for the adult nAChR in patients with MG.

Human T-cell leukemia virus type 1 Tax and cell cycle progression: role of cyclin D-cdk and p110Rb.

Human T-cell leukemia virus type 1 is etiologically linked to the development of adult T-cell leukemia and various human neuropathies. The Tax protein of human T-cell leukemia virus type I has been implicated in cellular transformation. Like other oncoproteins, such as Myc, Jun, and Fos, Tax is a transcriptional activator. How it mechanistically dysregulates the cell cycle is unclear. Previously, it was suggested that Tax affects cell-phase transition by forming a direct protein-protein complex with p16(INK4a), thereby inactivating an inhibitor of G1-to-S-phase progression. Here we show that, in T cells deleted for p16(INK4a), Tax can compel an egress of cells from G0/G1 into S despite the absence of serum. We also show that in undifferentiated myocytes, expression of Tax represses cellular differentiation. In both settings, Tax expression was found to increase cyclin D-cdk activity and to enhance pRb phosphorylation. In T cells, a Tax-associated increase in steady-state E2F2 protein was also documented. In searching for a molecular explanation for these observations, we found that Tax forms a protein-protein complex with cyclin D3, whereas a point-mutated and transcriptionally inert Tax mutant failed to form such a complex. Interestingly, expression of wild-type Tax protein in cells was also correlated with the induction of a novel hyperphosphorylated cyclin D3 protein. Taken together, these findings suggest that Tax might directly influence cyclin D-cdk activity and function, perhaps by a route independent of cdk inhibitors such as p16(INK4a).

Inflammatory genes are upregulated in expanded ataxin-3-expressing cell lines and spinocerebellar ataxia type 3 brains.

Spinocerebellar ataxia type 3 (SCA3) is a polyglutamine disorder caused by a CAG repeat expansion in the coding region of a gene encoding ataxin-3. To study putative alterations of gene expression induced by expanded ataxin-3, we performed PCR-based cDNA subtractive hybridization in a cell culture model of SCA3. In rat mesencephalic CSM14.1 cells stably expressing expanded ataxin-3, we found a significant upregulation of mRNAs encoding the endopeptidase matrix metalloproteinase 2 (MMP-2), the transmembrane protein amyloid precursor protein, the interleukin-1 receptor-related Fos-inducible transcript, and the cytokine stromal cell-derived factor 1alpha (SDF1alpha). Immunohistochemical studies of the corresponding or associated proteins in human SCA3 brain tissue confirmed these findings, showing increased expression of MMP-2 and amyloid beta-protein (Abeta) in pontine neurons containing nuclear inclusions. In addition, extracellular Abeta-immunoreactive deposits were detected in human SCA3 pons. Furthermore, pontine neurons of SCA3 brains strongly expressed the antiinflammatory interleukin-1 receptor antagonist, the proinflammatory cytokine interleukin-1beta, and the proinflammatory chemokine SDF1. Finally, increased numbers of reactive astrocytes and activated microglial cells were found in SCA3 pons. These results suggest that inflammatory processes are involved in the pathogenesis of SCA3.

Identification of substrate orienting and phosphorylation sites within tryptophan hydroxylase using homology-based molecular modeling.

Tryptophan hydroxylase (TPH) is the initial and rate-limiting enzyme in the biosynthesis of serotonin. The inherent instability of TPH has prevented a crystallographic structure from being resolved. For this reason, multiple sequence alignment-based molecular modeling was utilized to generate a full-length model of human TPH. Previously determined crystal coordinates of two highly homologous proteins, phenylalanine hydroxylase and tyrosine hydroxylase, were used as templates. Analysis of the model aided rational mutagenesis studies to further dissect the regulation and catalysis of TPH. Using rational site-directed mutagenesis, it was determined that Tyr235 (Y235), within the active site of TPH, appears to be involved as a tryptophan substrate orienting residue. The mutants Y235A and Y235L displayed reduced specific activity compared to wild-type TPH ( approximately 5 % residual activity). The K(m) of tryptophan for the Y235A (564 microM) and Y235L (96 microM) mutant was significantly increased compared to wild-type TPH (42 microM). In addition, kinetic analyses were performed on wild-type TPH and a deletion construct that lacks the amino terminal autoregulatory sequence (TPH NDelta15). This sequence in phenylalanine hydroxylase (residues 19 to 33) has previously been proposed to act as a steric regulator of substrate accessibility to the active site. Changes in the steady-state kinetics for tetrahydrobiopterin (BH(4)) and tryptophan for TPH NDelta15 were not observed. Finally, it was demonstrated that both Ser58 and Ser260 are substrates for Ca(2+)/calmodulin-dependent protein kinase II. Additional analysis of this model will aid in deciphering the regulation and substrate specificity of TPH, as well as providing a basis to understand as yet to be identified polymorphisms.

Induction of functional empty class I major histocompatibility complex glycoproteins by photoactivated 8-methoxypsoralen.

CD8+ cytotoxic T lymphocytes (CTLs) bind to and selectively lyse tumor cells via T-cell receptor recognition of distinctive peptide antigens presented in the context of surface major histocompatibility complex class I (MHC class I) glycoproteins. Several human and experimental animal tumors express distinctive MHC class I-associated peptides, which can be selectively targeted by specific CD8+ CTLs. Malignant cells expressing low quantities of these peptides are poor inducers of CTL responses. Therefore, we have developed a method of externally loading increased amounts of antigenic peptides onto MHC class I molecules. In order to induce "empty" fillable MHC class I molecules capable of binding antigenic peptides, we exposed transformed murine T cells (RMA) to low dose (3 joules/cm2) ultraviolet A energy and 8-methoxypsoralen (100 ng per ml). Presence of "empty" class I molecules was ascertained by "meltdown" or loss of the thermodynamically unstable cold-induced "empty" molecules as identified by cytofluorography at 37 degrees C. Retained function of "empty" molecules was determined by their stabilization through addition of peptides of the correct size and sequence motif, prior to exposure to physiologic temperature.

An isoform of ataxin-3 accumulates in the nucleus of neuronal cells in affected brain regions of SCA3 patients.

Autosomal dominant spinocerebellar ataxias (SCA) form a group of clinically and genetically heterogeneous neurodegenerative disorders. The defect responsible for SCA3/Machado-Joseph disease (MJD) has been identified as an unstable and expanded (CAG)n trinucleotide repeat in the coding region of a novel gene of unknown function. The MJD1 gene product, ataxin-3, exists in several isoforms. We generated polyclonal antisera against an alternate carboxy terminus of ataxin-3. This isoform, ataxin-3c, is expressed as a protein of approximately 42 kDa in normal individuals but is significantly enlarged in affected patients confirming that the CAG repeat is part of the ataxin-3c isoform and is translated into a polyglutamine stretch, a feature common to all known CAG repeat disorders. Ataxin-3 like immunoreactivity was observed in all human brain regions and peripheral organs studied. In neuronal cells of control individuals, ataxin-3c was expressed cytoplasmatically and had a somatodendritic and axonal distribution. In SCA3 patients, however, C-terminal ataxin-3c antibodies as well as anti-ataxin-3 monoclonal antibodies (1 H9) and anti-ubiquitin antibodies detected intranuclear inclusions (NIs) in neuronal cells of affected brain regions. A monoclonal antibody, 2B6, directed against an internal part of the protein, barely detected these NIs implying proteolytic cleavage of ataxin-3 prior to its transport into the nucleus. These findings provide evidence that the alternate isoform of ataxin-3 is involved in the pathogenesis of SCA3/MJD. Intranuclear protein aggregates appear as a common feature of neurodegenerative polyglutamine disorders.

In vivo preferential usage of TCR V beta 8 in Torpedo acetylcholine receptor immune response in the murine experimental model of myasthenia gravis.

The aim of our study was to determine the T cell receptor (TCR) V beta gene usage involved in the T cell response to Torpedo AChR in C57BL/6 mice. The specific proliferation towards AChR was found to be blocked by anti-V beta 8.1,2,3 and to a lesser extent by anti-V beta 5 mAbs, but not by the other antibodies used (anti-V beta 2, V beta 6, V beta 9). In addition, a significant expansion of CD4+ V beta 8+ cells was observed when lymph node cells from these primed mice were stimulated in vitro with purified AChR. Involvement of V beta 8 subfamilies was also explored in vivo. After 7 days of treatment, there was a striking inhibition of the proliferative response of cells from anti-V beta 8.1,2,3-treated mice and a moderate inhibition when using anti-V beta 8.1,2 and anti-V beta 8.2 antibodies. Thus our in vitro and in vivo analysis indicate that in C57Bl/6 mice, T cell response to AChR is restricted to few V beta TCR, mostly belonging to the V beta 8 sub-families.

Tax-dependent stimulation of G1 phase-specific cyclin-dependent kinases and increased expression of signal transduction genes characterize HTLV type 1-transformed T cells.

Human T cell leukemia virus protein induces T cells to permanent IL-2-dependent growth. These cells occasionally convert to factor independence. The viral oncoprotein Tax acts as an essential growth factor of transformed lymphocytes and stimulates the cell cycle in the G(1) phase. In T cells and fibroblasts Tax enhances the activity of the cyclin-dependent kinases (CDK) CDK4 and CDK6. These kinases, which require binding to cyclin D isotypes for their activity, control the G(1) phase. Coimmunoprecipitation from these cells revealed that Tax associates with cyclin D3/CDK6, suggesting a direct activation of this kinase. The CDK stimulation may account in part for the mitogenic Tax effect, which causes IL-2-dependent T cell growth by Tax. To address the conversion to IL-2-independent proliferation and to identify overexpressed genes, which contribute to the transformed growth, the gene expression patterns of HTLV-1-transformed T cells were compared with that of peripheral blood lymphocytes. Potentially overexpressed cDNAs were cloned, sequenced, and used to determine the RNA expression. Genes found to be up-regulated are involved in signal transduction (STAT5a, cyclin G(1), c-fgr, hPGT) and also glycoprotein synthesis (LDLC, ribophorin). Many of these are also activated during T cell activation and implicated in the regulation of growth and apoptosis. The transcription factor STAT5a, which is involved in IL-2 signaling, was strongly up-regulated only in IL-2-independent cells, thus suggesting that it contributes to factor-independent growth. Thus, the differentially expressed genes could cooperate with the Tax-induced cell cycle stimulation in the maintenance of IL-2-dependent and IL-2-independent growth of HTLV-transformed lymphocytes.

Interleukin-6 overproduction by cultured thymic epithelial cells from patients with myasthenia gravis is potentially involved in thymic hyperplasia.

Most patients with Myasthenia Gravis (MG) present a thymic hyperplasia characterized by the presence of lymphoid follicles. The acetylcholine receptor autoantigen, as well as autoantigen specific activated T and B cells found in the thymus, strongly suggest that auto-sensitization could take place in this organ. Since IL-6 is involved in T and B cell growth and differentiation, we thought that abnormal IL-6 expression by thymic epithelial cells (TEC) could be related to thymic hyperplasia in MG. In this paper, IL-6 protein and gene expression by cultured TEC from patients with MG were examined. TEC from patients presented a dramatic IL-6 hyperproduction phenotype as compared to controls when stimulated by exogenous signals such as LPS and cytokines (IL-1 beta, TNF-alpha) alone or in combination. Moreover, we observed a similar effect with a physiological signal such as the syngeneic lympho-epithelial cell contact. Autologous thymocytes stimulated normal and MG TEC IL-6 production in a time- and dose- dependent way, and with a higher magnitude in MG TEC compared to controls. In all stimulation conditions, induction of IL-6 production required protein synthesis and was associated with increased IL-6 mRNA level expression as assessed by computer-aided quantification after in situ mRNA hybridization. In addition, recombinant IL-6 induced in vitro growth of TEC, demonstrating that IL-6 is a possible autocrine growth factor for these cells. This deregulated IL-6 production as well as the ability of TEC to use it as a growth factor may be of pathophysiological relevance in MG. It provides an explanation for morphological changes of the thymus and may have a key role in initiation, exacerbation and ongoing of the autoimmune response in MG. Therefore this study extends our current understanding of the molecular pathophysiology of MG.

Psoralen-protein photochemistry--a forgotten field.

8-Methoxypsoralen in combination with long wavelength ultraviolet light is employed for the treatment of several cutaneous disorders, such as psoriasis, vitiligo and mycosis fungoides. It is common to attribute the efficacy of the photochemotherapy to the formation of psoralen DNA photoadducts. Thus, the main research effort has been directed towards the elucidation of nucleic acid photochemistry and related subsequent events (mutagenicity, toxicity). However, psoralens have been shown to undergo photoaddition reactions with other cellular components. In this review the status of psoralen-DNA photobiology is briefly summarized. The main focus, however, is on a survey of psoralen photochemical modification of proteins and the ways by which these additional photobiological events can impact the antigenicity and potentially immunogenicity of treated cells. Some preliminary results show the extent of psoralen-amino acid photoadduct formation and their impact on enzymatic processing.

Treatment with 8-MOP and UVA enhances MHC class I synthesis in RMA cells: preliminary results.

The response of psoriasis and cutaneous T-cell lymphoma to treatment with 8-methoxypsoralen (8-MOP) and long wavelength ultraviolet light (UVA) is only partly understood. Psoralens form photoadducts within the DNA after activation by UVA and this damage leads to the inhibition of DNA synthesis. Additionally, it has been shown that different forms of DNA damage can induce a stress response, leading to upregulation of selected products. Among these are the major histocompatibility complex (MHC) class I genes. Thus the aim of the present study was to assess the rate of synthesis of MHC class I proteins in murine T-cell lymphoma cells (RMA) after treatment with 8-MOP and UVA. RMA cells were treated with 8-MOP (50-200 ng ml-1) and UVA (1 J.cm-2) and metabolically labelled with 35S-methionine 4 and 24 h after treatment. MHC class I synthesis was determined by immunoprecipitation of the cell lysates with an anti-Kb monoclonal antibody, Y3. After 4 h, treated and untreated cells demonstrated no differences in the rate of MHC class I synthesis. However, after 24 h a dose-dependent increase in MHC class I synthesis was observed. This increase in MHC class I expression could be responsible, at least partly, for the responses observed in patients treated with photopheresis.

The specific effects of 8-methoxypsoralen photoadducts on cell growth: HPLC analysis of monoadduct and crosslink formation in cells exposed to split-dose treatment.

The effects of 8-methoxypsoralen (8-MOP) monoadducts and crosslinks on growth and viability of mastocytoma cells were investigated. To induce monoadduct formation (4',5'-monoadducts and 3,4-monoadducts), the cells were incubated with 8-MOP (1 microgram ml-1) and exposed to 419 nm radiation, resulting in the formation of more than 96% monoadducts. After washing and resuspension, the cells were exposed to a small dose of long-wavelength UV radiation (UVA, 2 J cm-2) to convert monoadducts into crosslinks. Similar adduct levels were obtained after either 8-MOP plus visible light treatment or 8-MOP plus split-dose protocol. Cells treated with 419 nm light resumed normal growth rates more rapidly than cells which also received the UVA dose. High performance liquid chromatography (HPLC) analysis of DNA obtained from each group of cells showed that the UVA step resulted in an increase in crosslinks from 3.2% after 419 nm radiation to 56.5% after UVA irradiation.

Relationships of the 2642 deletion polymorphism (delta 2642) in the huntingtin gene with the CAG repeat expansion length and age at onset of the disease.

The deletion of 3bp at codon positions 2642-2645 (delta 2642) of the gene mutated in Huntington's disease (HD) was analysed on the normal (N) and HD chromosomes of 79 French families affected with HD, and previously typed for the (CAG)n repeats. delta 2642 Polymorphism has been found over-represented on HD chromosomes, the relative risk of HD with the deletion being at a value of 8.26. In this study, the presence of the deleted allele on HD chromosomes increases the (CAG)n number (47.93 +/- 1.80 versus 43.50 +/- 2.78) and decreases the age of onset (41.34 +/- 2.09 versus 36.90 +/- 2.41) in the patients with versus without delta 2642; so the deletion may add to the severity of the disease. Our studies of delta 2642 on N chromosomes confirm that the deletion event occurs on N chromosomes with a (CAG)n allele length at the upper end of the normal size range.

Molecular genetics of inherited diseases involving human chromosome 4.

Two molecular genetic strategies have widely been employed to characterize candidate genes for human inherited diseases; identification of disease genes via positional cloning and characterization of altered candidate genes in affected persons. Both approaches allowed to uncover disease genes. A well-known example for positional cloning is the identification of the Huntington's disease (HD) gene on human chromosome 4. In other diseases such as piebaldism, Hurler/Scheie syndrome and a form of autosomal recessive retinitis pigmentosa, the disease gene has first been analyzed and later been localized to human chromosome 4. Steady progress in the human genome project permits to combine affected families pointing to the chromosomal localization of the disease causing defects. Then the genes are investigated that are already mapped to this particular region. Accordingly the achondrodysplasia gene has been identified within six months after its chromosomal localization. In order to evaluate cloned genes as potential candidates for disorders linked to chromosome 4, it is important to assign all genes to chromosomal (sub)regions. Furthermore in excess of 140 closely spaced microsatellites on chromosome 4 as well as many "expressed sequence tags" will help to narrow in on additional disease genes.

Sustained calcium signalling and caspase-3 activation involve NMDA receptors in thymocytes in contact with dendritic cells.

L-glutamate, the major excitatory neurotransmitter, also has a role in non-neuronal tissues and modulates immune responses. Whether NMDA receptor (NMDAR) signalling is involved in T-cell development is unknown. In this study, we show that mouse thymocytes expressed an array of glutamate receptors, including NMDARs subunits. Sustained calcium (Ca(2+)) signals and caspase-3 activation in thymocytes were induced by interaction with antigen-pulsed dendritic cells (DCs) and were inhibited by NMDAR antagonists MK801 and memantine. NMDARs were transiently activated, triggered the sustained Ca(2+) signal and were corecruited with the PDZ-domain adaptor postsynaptic density (PSD)-95 to thymocyte-DC contact zones. Although T-cell receptor (TCR) activation was sufficient for relocalization of NMDAR and PSD-95 at the contact zone, NMDAR could be activated only in a synaptic context. In these T-DC contacts, thymocyte activation occurred in the absence of exogenous glutamate, indicating that DCs could be a physiological source of glutamate. DCs expressed glutamate, glutamate-specific vesicular glutamate transporters and were capable of fast glutamate release through a Ca(2+)-dependent mechanism. We suggest that glutamate released by DCs could elicit focal responses through NMDAR-signalling in T cells undergoing apoptosis. Thus, synapses between T and DCs could provide a functional platform for coupling TCR activation and NMDAR signalling, which might reflect on T-cell development and modulation of the immune response.