Responses of soil fungi to logging and oil palm agriculture in Southeast Asian tropical forests.

Human land use alters soil microbial composition and function in a variety of systems, although few comparable studies have been done in tropical forests and tropical agricultural production areas. Logging and the expansion of oil palm agriculture are two of the most significant drivers of tropical deforestation, and the latter is most prevalent in Southeast Asia. The aim of this study was to compare soil fungal communities from three sites in Malaysia that represent three of the most dominant land-use types in the Southeast Asia tropics: a primary forest, a regenerating forest that had been selectively logged 50 years previously, and a 25-year-old oil palm plantation. Soil cores were collected from three replicate plots at each site, and fungal communities were sequenced using the Illumina platform. Extracellular enzyme assays were assessed as a proxy for soil microbial function. We found that fungal communities were distinct across all sites, although fungal composition in the regenerating forest was more similar to the primary forest than either forest community was to the oil palm site. Ectomycorrhizal fungi, which are important associates of the dominant Dipterocarpaceae tree family in this region, were compositionally distinct across forests, but were nearly absent from oil palm soils. Extracellular enzyme assays indicated that the soil ecosystem in oil palm plantations experienced altered nutrient cycling dynamics, but there were few differences between regenerating and primary forest soils. Together, these results show that logging and the replacement of primary forest with oil palm plantations alter fungal community and function, although forests regenerating from logging had more similarities with primary forests in terms of fungal composition and nutrient cycling potential. Since oil palm agriculture is currently the mostly rapidly expanding equatorial crop and logging is pervasive across tropical ecosystems, these findings may have broad applicability.

Dual mycorrhizal colonization of forest-dominating tropical trees and the mycorrhizal status of non-dominant tree and liana species.

The contribution of mycorrhizal associations to maintaining tree diversity patterns in tropical rain forests is poorly known. Many tropical monodominant trees form ectomycorrhizal (EM) associations, and there is evidence that the EM mutualism contributes to the maintenance of monodominance. It is assumed that most other tropical tree species form arbuscular mycorrhizal (AM) associations, and while many mycorrhizal surveys have been done, the mycorrhizal status of numerous tropical tree taxa remains undocumented. In this study, we tested the assumption that most tropical trees form AM associations by sampling root vouchers from tree and liana species in monodominant Dicymbe corymbosa forest and an adjacent mixed rain forest in Guyana. Roots were assessed for the presence/ absence of AM and EM structures. Of the 142 species of trees and lianas surveyed, three tree species (the mono-dominant D. corymbosa, the grove-forming D. altsonii, and the non-dominant Aldina insignis) were EM, 137 were exclusively AM, and two were non-mycorrhizal. Both EM and AM structures wer e observed in D. corymbosa and D. altsonii. These results provide empirical data supporting the assumption that most tropical trees form AM associations for this region in the Guiana Shield and provide the first report of dual EM/AM colonization in Dicymbe species. Dual colonization of the Dicymbe species should be further explored to determine if this ability contributes to the establishment and maintenance of site dominance.

Repression of IL-2 promoter activity by the novel basic leucine zipper p21SNFT protein.

IL-2 is the major autocrine and paracrine growth factor produced by T cells upon T cell stimulation. The inducible expression of IL-2 is highly regulated by multiple transcription factors, particularly AP-1, which coordinately activate the promoter. Described here is the ability of the novel basic leucine zipper protein p21SNFT to repress AP-1 activity and IL-2 transcription. A detailed analysis of the repression by p21SNFT repression on the IL-2 promoter distal NF-AT/AP-1 site demonstrates that it can bind DNA with NF-AT and Jun, strongly suggesting that it represses NF-AT/AP-1 activity by competing with Fos proteins for Jun dimerization. The importance of this repression is that p21SNFT inhibits the trans-activation potential of protein complexes that contain Jun, thereby demonstrating an additional level of control for the highly regulated, ubiquitous AP-1 transcription factor and the IL-2 gene.

IL-2-mediated cell cycle progression and inhibition of apoptosis does not require NF-kappa B or activating protein-1 activation in primary human T cells.

The IL-2 growth hormone is the major growth factor of activated T lymphocytes during a developing immune response. IL-2 is required not only for cell cycle progression but also to protect Ag-activated T cells from programmed cell death. In several cell types, activation of NF-kappa B and/or activating protein-1 (AP-1) has been demonstrated to be extremely important in blocking apoptosis. To determine whether either or both of these transcription factors are involved in cell survival or cell cycle progression in response to IL-2, primary human T cells responsive to the growth factor were analyzed for NF-kappa B and AP-1 activation. The current study clearly demonstrates that IL-2 does not induce I kappa B alpha degradation or NF-kappa B activation in primary human T cells that respond to IL-2 by entering the cell cycle and avoiding apoptosis. Similarly, IL-2 neither activates JNK nor increases AP-1 binding activity to a consensus o-tetradecanoylphorbol 13-acetate (TPA) response element. On the other hand, the growth factor does induce the activation of STAT3 and STAT5 in these cells, as has been previously demonstrated. These data show that neither NF-kappa B nor AP-1 activation is required for IL-2-mediated survival or cell cycle progression in activated primary human T cells.

Involvement of Rel, Fos, and Jun proteins in binding activity to the IL-2 promoter CD28 response element/AP-1 sequence in human T cells.

CD28 is an important costimulatory molecule in the activation of human T cells. Costimulation of T cells through both the Ag receptor and CD28 leads to high level IL-2 production, which is vital to the development of an immune response in vivo. Previous reports have suggested the CD28 stimulation contributes to the activation of the IL-2 promoter by up-regulating the activity of several transcription factors, including AP-1 and nuclear factor-kappaB (NF-kappaB)/Rel family members as well as an uncharacterized transcription factor called CD28 response complex. While several lines of investigation have suggested that NF-kappaB/Rel family members make up the CD28 response complex transcription factor, other work has not supported this conclusion. Recent studies suggest that the CD28 response element (CD28RE) does not function independently but works instead in conjunction with the adjacent promoter proximal AP-1-binding site and this hypothesis is confirmed here. Also in the current study, binding activity to the CD28RE/AP-1 sequence of the IL-2 promoter is evaluated. Although four specific complexes can be detected binding to this sequence, only one of these complexes is specific for both the CD28RE and the adjacent AP-1 site. Of the NF-kappaB/Rel family members tested, this CD28RE/AP-1-specific complex contains predominantly c-Rel, despite the fact that both p50 and RelA can efficiently bind to the CD28RE. c-Fos and c-Jun are also found in this CD28RE/AP-1-specific complex. These data indicate that functional complexes encompassing both the CD28RE and the AP-1-binding sites influence IL-2 promoter activity in CD28-costimulated T cells.

Requirements for interleukin 2 promoter transactivation by the Tax protein of human T-cell leukemia virus type 1.

The Tax protein of human T-cell leukemia virus type 1 (HTLV-1) upregulates the expression of several cellular genes by activating members of both the NF-kappaB and bZIP families of transcription factors. Recent studies demonstrate that the CD28 response element (CD28RE) of the interleukin 2 (IL-2) promoter is the site upregulated by Tax in stimulated T cells. Although some reports suggest that this site is transactivated by NF-kappaB family members, others disagree, leaving the identity of the transcription factor(s) binding the CD28RE unclear. The studies presented here further characterize the response of the IL-2 promoter and CD28RE to the HTLV-1 Tax protein and demonstrate that the TATA-proximal AP-1 binding site of the IL-2 promoter is also necessary for Tax transactivation in stimulated Jurkat cells. In contrast to its upregulation of the IL-2 promoter which requires T-cell stimulation, Tax transactivates the isolated CD28RE-AP-1 element without stimulation but is greatly synergized by calcium ionophore and phorbol ester. Additionally, transactivation of the IL-2 promoter requires the Tax activation domain involved in upregulation of bZIP-enhanced transcription while the NF-kappaB-activating domain of Tax is dispensable. Interestingly, both domains appear to be necessary for the activation of the isolated CD28RE-AP-1 sequence in the context of a heterologous promoter construct. This strongly suggests that activation of NF-kappaB is insufficient to activate transcription via the CD28RE-AP-1 element of the IL-2 promoter and that a different transcription factor, upregulated via the activation domain of the HTLV-1 Tax protein, may be involved.

The effect of IL-2 treatment on transcriptional attenuation in proto-oncogenes pim-1 and c-myb in human thymic blast cells.

IL-2 is the major mitogenic cytokine for mature human T cells. This growth factor has been shown previously to induce the expression of a number of genes, including structural proteins, proto-oncogenes, and metabolic enzymes. Multiple mechanisms, including increases in mRNA stability, protein synthesis, and new transcriptional initiation, have been studied to determine how IL-2 induces such a wide variety of genes. The following studies show that a release of transcriptional attenuation is important in IL-2-induced gene expression. A thymic blast cell system was developed and used to demonstrate that IL-2-deprived cells have a marked attenuation of transcription in the 3' ends of the pim-1 and c-myb genes. IL-2 stimulation removes this attenuation and leads to read-through transcription. This effect is gene-specific, as demonstrated by the fact that GAPDH is not attenuated in unstimulated cells. The IL-2-mediated relief of attenuation occurs within 1 h of IL-2 stimulation and is insensitive to the translation inhibitor cycloheximide, suggesting that new protein synthesis is not necessary. Further, the effect is insensitive to the immunosuppressant cyclosporin A, but is sensitive to rapamycin and the tyrosine kinase inhibitor genistein. These studies demonstrate that release of transcription attenuation is a mechanism used to induce gene expression in response to IL-2 treatment.

Interaction between G proteins and tyrosine kinases upon T cell receptor.CD3-mediated signaling.

Engagement of the T cell receptor (TCR).CD3 complex results in the induction of multiple intracellular events, with protein tyrosine kinases playing a pivotal role in their initiation. Biochemical studies also exist suggesting the involvement of heterotrimeric GTP-binding proteins (G proteins); however, the functional consequence of this participation in TCR.CD3-mediated signaling is unresolved. Here, we report TCR.CD3-mediated guanine nucleotide exchange among the 42-kDa G protein alpha subunits of the G alpha q/11 family, their physical association with CD3 epsilon, and the G alpha 11-dependent activation of phospholipase C beta. Protein tyrosine kinase inhibitors, however, abrogate TCR.CD3-mediated G protein activation. Quite interesting is the observation that cells transfected with a function-deficient mutant of G alpha 11 display diminished tyrosine phosphorylation of TCR.CD3 zeta and epsilon chains, as well as ZAP-70, upon anti-CD3 antibody triggering. These data indicate the involvement of the G alpha q/11 family in TCR.CD3 signaling at a step proximal to the receptor and suggest a reciprocal regulation between tyrosine kinases and G proteins in T cells.

Localization of the Chinese hamster MHC locus to chromosome 1q17-->q18 by fluorescence in situ hybridization.

Comparative gene mapping analysis in mammals suggests that the major histocompatibility complex (MHC) genes map syntenic with genes, such as glyoxylase 1 (GLO1). In man, the MHC locus and other genes of this syntenic group map to chromosome band 6p21.3, and in mouse, these genes map to chromosome 17. In the hamster, however, only the GLO1 gene has been localized; GLO1 maps to chromosome 1, suggesting that the genes within the MHC locus also map to this chromosome. We have localized the hamster MHC class I genes to chromosome band 1q17-->q18 by fluorescence in situ hybridization (FISH). These results suggest that GLO1 and other syntenic genes also lie within this chromosome region.

Influence of human T-cell leukemia virus type I tax and rex on interleukin-2 gene expression.

The X region of human T-cell leukemia virus type I (HTLV-I) encodes two proteins that regulate viral gene expression. The tax protein is the product of the transactivator gene and has been shown to up-regulate the expression of some cellular genes controlling T-cell replication, including that of the interleukin-2 (IL-2) T-cell growth hormone and the alpha chain of its receptor (IL-2R). Several studies have shown that tax transactivation of the IL-2R alpha-chain promoter is mediated by binding sites for the transcriptional activator NF-kappa B, and this mechanism has also been implicated in the tax activation of IL-2 promoter activity. The rex gene product of HTLV-I regulates viral protein production by influencing mRNA expression and has been implicated in the stabilization of IL-2R alpha-chain mRNA. In the present studies, the ability of the tax and rex proteins to transactivate IL-2 gene expression has been reinvestigated. The ability of the tax protein to transactivate IL-2 promoter activity appears, at least in part, to be mediated by the recognition sequence for a DNA-binding complex known as CD28RC. Consistent with this hypothesis is the observation that tax-mediated activation of IL-2 gene expression is resistant to the immunosuppressive affects of cyclosporin A, a property postulated for the CD28RC binding complex. Unexpectedly, this tax-mediated up-regulation of IL-2 expression is synergized by the presence of the rex protein. These findings demonstrate that transactivation of IL-2 gene expression by tax is augmented by mechanisms distinct from NF-kappa B and raise the possibility that rex, as well as tax, contributes to the oncogenic capability of HTLV-I by altering the expression of the IL-2 gene in T cells infected with this retrovirus.

Influence of activating stimulus on functional phenotype: interleukin 2 mRNA accumulation differentially induced by ionophore and receptor ligands in subsets of murine T cells.

We have investigated the linkage between CD4/CD8 phenotype and programming for specific responses in primary T-cell populations. In situ hybridization has been used to determine the frequency of cells competent to express the interleukin 2 (IL-2) gene after short-term stimulation with various polyclonal activators. The effects of the T-cell receptor ligands Con A and anti-CD3 monoclonal antibody were compared with those of a calcium ionophore that bypasses membrane receptors altogether. Induction with a calcium ionophore and phorbol ester revealed that potential IL-2 producers not only constitute greater than 85% of the cells with a CD4+ "helper/inducer" phenotype but also constitute over half of the cells with a CD8+ "killer/suppressor" phenotype. There is no defect in the ability of these CD8+ cells to accumulate IL-2 transcripts under these conditions. By contrast, in response to phorbol ester and either Con A or anti-CD3, the CD8+ cells show an abortive IL-2 production response with rapid disappearance of IL-2 mRNA. This results in substantially lower yields of IL-2 per cell than is made by CD4+ cells in response to the same stimuli. The extent to which these populations appear to have diverged in function thus depends on the stimulus used to trigger the response. The results suggest that differences in signal transduction or posttranscriptional regulatory mechanisms, rather than effector gene inducibility per se, may initially underlie the commitment of CD4+ and CD8+ cells to distinct functional roles.

Differential regulation of T cell receptor gamma genes in immature thymocyte populations.

Immature thymocytes that lack both Lyt-2 (CD8) and L3T4 (CD4) expression can respond rapidly to stimulation with phorbol ester and calcium ionophore by expressing some gene products characteristic of mature, activated T cells. Here we studied the effect of such short-term stimulation on the number of copies per cell of RNA for components of the T cell receptor complex. Although, upon stimulation, mRNAs for T cell receptor beta chain accumulated to higher levels, the cells did not rapidly increase their expression of alpha-chain transcripts from rearranged or germ-line genes. Transcripts from the C gamma 1 (C gamma 13.4) and C gamma 2 (C gamma 10.5) genes were differentially regulated. The rarer C gamma 1 transcripts were strongly induced, while the initially abundant C gamma 2 transcripts showed a modest decrease in transcripts per cell within 24 h. Thus, the ratio of these two transcripts could be shifted dramatically prior to any significant change in the cellular composition of the population. These results suggest regulatory processes that may contribute to the observed expression of gamma products in vitro or in normal development.

Inducibility of interleukin-2 RNA expression in individual mature and immature T lymphocytes.

Expression of the gene for the T-cell growth hormone, interleukin 2 (IL2), is subject to at least two types of control. It is not only tissue specific, i.e. restricted to T lymphocytes, but also strictly dependent upon activation of the producing T cell. In mature cells, IL2 production is usually triggered via the cell surface receptor for antigen. To study the regulation of the murine IL2 gene in T-cell populations of differing stages of maturation, we have used a calcium ionophore in conjunction with the phorbol ester, TPA, to stimulate IL2 gene transcription while bypassing the requirement for triggering through a mature cell surface receptor. We have combined in situ hybridization with RNA probe protection analyses to quantitate accumulated cytoplasmic IL2 RNA and to identify the cells capable of inducing the IL2 gene in mature, immature and precursor T-cell populations. We report evidence for a distinction between the IL2 mRNA induction responses of different T cells, according to their maturation state and/or functional subclass. Mature splenic T cells that make IL2 can accumulate IL2 transcripts to more than 100 copies per cell. However, we find that many T-lineage cells, especially in immature populations, show induction-dependent IL2 gene expression but only accumulate low levels of IL2 mRNA per cell.

Structure of a class I gene from Syrian hamster.

Syrian hamsters possess a multigene class I family yet fail to perform several associative immunologic functions. In an attempt to determine whether representative hamster genes are structurally functional, we have cloned two closely linked class I-like genes and determined the complete sequence of the 5' member. Its exon organization is similar to that seen in mouse and man, although only two intracytoplasmic domains are encoded instead of the usual three. Comparison of the predicted amino acid sequence and the 3' untranslated region to mouse and human genes suggest along with the linkage data that the hamster gene may be related to either or both K and Qa region genes but probably not to D and L region genes.

Phylogenetic conservation of immunoglobulin heavy chains: direct comparison of hamster and mouse Cmu genes.

We have analyzed the JH-Cmu locus of the Syrian hamster by DNA cloning and sequencing. The single Cmu gene is highly homologous to that of the mouse. The hamster equivalents of the JH and switch (S) recombination regions are arranged as in the mouse, but surprisingly are not highly conserved. Also unlike its close murine relative, the Smu regions among inbred hamster strains are not polymorphic. The complete nucleotide sequence of hamster and mouse Cmu genes have been compared to partial Cmu sequences of other species. Conservation within a portion of the 3' untranslated region may signify functional requirements for 3' end processing. Mutational frequencies within exons and introns of hamster and mouse do not support the theory that the rate of DNA transitions to transversions decreases with evolutionary distance.

Syrian hamster DNA shows limited polymorphism at class I-like loci.

The class I gene products of the Syrian hamster major histocompatibility complex are unique in that they lack functionally detectable polymorphism. Mouse cDNA and hamster genomic probes were used to analyze the hamster class I gene family using genomic Southern hybridization. These studies revealed that the hamster possesses a complex class I multigene family and that it shares extensive sequence homology with the corresponding mouse sequences. Unlike the mouse, however, the Syrian hamster demonstrates only limited restriction endonuclease polymorphism in these genes. These results suggest that the lack of detectable polymorphism in this species is directly related to limited DNA polymorphism. The data presented here support the hypothesis that this species has undergone an evolutionary bottleneck, i.e., that all surviving members of the species arose from a limited number of progenitors.

kappa/lambda Shifts do not occur during maturation of murine B cells.

We have used highly specific affinity-purified antibodies against mouse kappa- and lambda chains in conjunction with both immunofluorescence analysis on the FACS and enzymatic radioiodination of murine splenocytes and bone marrow cells. Our results indicate that the kappa/lambda ratio of cell surface immunoglobulin is constant during the ontogenetic development of B cells, i.e., a shift in the kappa/lambda ratio does not occur during B cell maturation. Our results suggest that the events controlling kappa and lambda expression on murine B cells are decided very early in ontogeny, before significant antigenic selection.