Conformational switching of Escherichia coli RNA polymerase-promoter binary complex is facilitated by elongation factor GreA and GreB

BACKGROUND

The initiation arrest at a modified lambdaPR promoter is caused by irreversible divergence of the reaction pathway into productive and arrested branches. Escherichia coli GreA and GreB induce cleavage of the nascent transcript and relieve arrest in elongation. They also reduce abortive synthesis at several promoters and relieve initiation arrest. Their mechanism of action during initiation, and its relationship to the branched initiation pathway are unknown.

RESULTS

The Gre factors mitigated initiation arrest only when they were added to the binary complex of the holoenzyme bound to the lambdaPR promoter, prior to RNA synthesis. They exerted little effect when they were added to ternary initiation complexes. They accelerated the exchange of the binary complex with its free components by 6-9-fold. When they are present, a high concentration of the initiating nucleotide increased yield of the full-length transcript, whereas a low concentration did not.

CONCLUSIONS

All the results presented above can be explained by a model where the productive and arrested pathways diverge at the binary complex stage. The Gre factors relieve the initiation arrest by introducing reversibility between subspecies of the binary complex that are precursors of the two pathways. RNA cleavage is unlikely to cause relief of initiation arrest.

Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA

Nascent RNA encoded by putL, a cis-acting antitermination site of bacteriophage HK022, increases readthrough of terminators by directly modifying the transcript elongation complex. To characterize the interaction between the antiterminator RNA and RNA polymerase, we stalled the elongation complex downstream of putL and determined the sensitivity of the transcript to ribonuclease cleavage. Part of PutL RNA was protected from cleavage by wild-type polymerase, but not by a mutant with a defect in put-dependent antitermination. We also exposed the stalled complex to oligonucleotides complementary to putL RNA, restarted transcription, and measured antitermination. Some, but not all, complementary oligonucleotides inhibited antitermination. Finally, cleavage of the RNA between putL and the 3'-end released putL RNA from the stalled complex and prevented antitermination.

IkappaB family members function by different mechanisms

The IkappaB family of proteins regulates NF-kappaB-dependent transcription by inhibiting DNA binding and localizing these factors to the cell cytoplasm. IkappaBalpha does this by shifting the balance between nuclear import of Rel proteins and their export from the nucleus. Here we show that, unlike IkappaBalpha, IkappaBbeta and IkappaBepsilon appear to sequester p65 or c-Rel in the cytoplasm by inhibiting nuclear import. Furthermore, because IkappaBbeta does not undergo nucleocytoplasmic shuttling, it cannot remove nuclear proteins like IkappaBalpha does. We conclude that the mechanism of action differs among IkappaB family members.

Heptad-repeat regions of respiratory syncytial virus F1 protein form a six-membered coiled-coil complex

The Respiratory Syncytial Virus (RSV) fusogenic glycoprotein F(1) was characterized using biochemical and biophysical techniques. Two heptad-repeat (HR) regions within F(1) were shown to interact. Proteinase-K digestion experiments highlight the HR1 region (located proximal to the fusion peptide sequence) of the F(1) protein to which an HR2-derived (located proximal to the membrane-spanning domain) peptide binds, thus protecting both the protein and peptide from digestion. Solution-phase analysis of HR1-derived peptides shows that these peptides adopt helical secondary structure as measured by circular dichroism. Sedimentation equilibrium studies indicate that these HR1 peptides self-associate in a monomer/trimer equilibrium with an association constant of 5.2 x 10(8) M(-2). In contrast, HR2-derived peptides form random monomers in solution. CD analysis of mixtures containing peptides from the two regions demonstrate their propensity to interact and form a very stable (T(m) = 87 degrees C), helical (86% helicity) complex comprised of three HR1 and three HR2 members.

Functional analysis of the murine TCR beta-chain gene enhancer

The TCR beta-chain gene enhancer activates transcription and V(D)J recombination in immature thymocytes. In this paper we present a systematic analysis of the elements that contribute to the activity of the murine TCR beta enhancer in mature and immature T cell lines. We identified a region containing the beta E4, beta E5, and beta E6 motifs as the essential core of the TCR beta enhancer in pro-T cells. In mature cells, the core enhancer had low activity and required, in addition, either 5' or 3' flanking sequences whose functions may be partially overlapping. Mutation of any of the six protein binding sites located within the beta E4-beta E6 elements essentially abolished enhancer activity, indicating that this core enhancer contained no redundant elements. The beta E4 and beta E6 elements contain binding sites for ETS-domain proteins and the core binding factor. The beta E5 element bound two proteins that could be resolved chromatographically and that were both essential for enhancer activity.

Effects of Pinus sylvestris root growth and mycorrhizosphere development on bacterial carbon source utilization and hydrocarbon oxidation in forest and petroleum-contaminated soils

The hypothesis that Pinus sylvestris L. root and mycorrhizosphere development positively influences bacterial community-linked carbon source utilization, and drives a concomitant reduction in mineral oil levels in a petroleum hydrocarbon- (PHC-) contaminated soil was confirmed in a forest ecosystem-based phytoremediation simulation. Seedlings were grown for 9 months in large petri dish microcosms containing either forest humus or humus amended with cores of PHC-contaminated soil. Except for increased root biomass in the humus/PHC treatment, there were no other significant treatment-related differences in plant growth and needle C and N status. Total cell and culturable bacterial (CFU) densities significantly increased in both rhizospheres and mycorrhizospheres that actively developed in the humus and PHC-contaminated soil. Mycorrhizospheres (mycorrhizas and extramatrical mycelium) supported the highest numbers of bacteria. Multivariate analyses of bacterial community carbon source utilization profiles (Biolog GN microplate) from different rhizosphere, mycorrhizosphere, and bulk soil compartments, involving principal component and correspondence analysis, highlighted three main niche-related groupings. The respective clusters identified contained bacterial communities from (i) unplanted bulk soils, (ii) planted bulk PHC and rhizospheres in PHC-contaminated soils, and (iii) planted bulk humus and rhizosphere/mycorrhizosphere-influenced humus, and mycorrhizosphere-influenced PHC contaminated soil. Correspondence analysis allowed further identification of amino acid preferences and increased carboxylic/organic acid preferences in rhizosphere and mycorrhizosphere compartments. Decreased levels of mineral oil (non-polar hydrocarbons) were detected in the PHC-contaminated soil colonized by pine roots and mycorrhizal fungi. These data further support our view that mycorrhizosphere development and function plays a central role in controlling associated bacterial communities and their degradative activities in lignin-rich forest humus and PHC-contaminated soils.

Polymerase arrest at the lambdaP(R) promoter during transcription initiation

During transcription initiation by Escherichia coli RNA polymerase, a fraction of the homogeneous enzyme population has been kinetically shown to form two types of nonproductive complexes at some promoters: moribund complexes, which produce only abortive transcripts, and fully inactive ternary complexes (Kubori, T., and Shimamoto, N. (1996) J. Mol. Biol. 256, 449-457). Here we report biochemical isolation of the complexes arrested at the lambdaP(R) promoter and an analysis of their structure by DNA and protein footprintings. We found that the isolated promoter-arrested complexes retain a stoichiometric amount of sigma(70) subunit. Exonuclease III footprints of the arrested complexes are backtracked compared with that of the binary complex, and KMnO(4) footprinting reveals a decrease in the melting of DNA in the promoter region. Protein footprints of the retained sigma(70) have shown a more exposed conformation in region 3, compared with binary complexes. This feature is similar to that of the complexes arrested in inactive state during transcription elongation, indicating the existence of a common inactivating mechanism during transcription initiation and elongation. The possible involvement of the promoter arrest in transcriptional regulation is discussed.

Cytoplasmic sequestration of rel proteins by IkappaBalpha requires CRM1-dependent nuclear export

Rel and IkappaB protein families form a complex cellular regulatory network. A major regulatory function of IkappaB proteins is to retain Rel proteins in the cell cytoplasm. In addition, IkappaB proteins have also been postulated to serve nuclear functions. These include the maintenance of inducible NF-kappaB-dependent gene transcription, as well as termination of inducible transcription. We show that IkappaBalpha shuttles between the nucleus and the cytoplasm, utilizing the nuclear export receptor CRM1. A CRM1-binding export sequence was identified in the N-terminal domain of IkappaBalpha but not in that of IkappaBbeta or IkappaBepsilon. By reconstituting major aspects of NF-kappaB-IkappaB sequestration in yeast, we demonstrate that cytoplasmic retention of p65 (also called RelA) by IkappaBalpha requires Crm1p-dependent nuclear export. In mammalian cells, inhibition of CRM1 by leptomycin B resulted in nuclear localization of cotransfected p65 and IkappaBalpha in COS cells and enhanced nuclear relocation of endogenous p65 in T cells. These observations suggest that the main function of IkappaBalpha is that of a nuclear export chaperone rather than a cytoplasmic tether. We propose that the nucleus is the major site of p65-IkappaBalpha association, from where these complexes must be exported in order to create the cytoplasmic pool.

An unusual case of choriocarcinoma following live term pregnancy

Post-term choriocarcinoma is an infrequent event with poor prognosis. The diagnosis is usually delayed due to failure to recognise the mode of presentation of this disease. Being a rare occurrence, limited data is available regarding its clinical features. The choriocarcinoma in our patient presented as an isolated huge pedunculated growth over the uterine serosa without intrauterine involvement and distant metastasis.

Cell-specific activation of nuclear factor-kappaB by the parasite Trypanosoma cruzi promotes resistance to intracellular infection

The transcription factor nuclear factor-kappaB (NF-kappaB) is central to the innate and acquired immune response to microbial pathogens, coordinating cellular responses to the presence of infection. Here we demonstrate a direct role for NF-kappaB activation in controlling intracellular infection in nonimmune cells. Trypanosoma cruzi is an intracellular parasite of mammalian cells with a marked preference for infection of myocytes. The molecular basis for this tissue tropism is unknown. Trypomastigotes, the infectious stage of T. cruzi, activate nuclear translocation and DNA binding of NF-kappaB p65 subunit and NF-kappaB-dependent gene expression in epithelial cells, endothelial cells, and fibroblasts. Inactivation of epithelial cell NF-kappaB signaling by inducible expression of the inhibitory mutant IkappaBaM significantly enhances parasite invasion. T. cruzi do not activate NF-kappaB in cells derived from skeletal, smooth, or cardiac muscle, despite the ability of these cells to respond to tumor necrosis factor-alpha with NF-kappaB activation. The in vitro infection level in these muscle-derived cells is more than double that seen in the other cell types tested. Therefore, the ability of T. cruzi to activate NF-kappaB correlates inversely with susceptibility to infection, suggesting that NF-kappaB activation is a determinant of the intracellular survival and tissue tropism of T. cruzi.

Multiple neurilemmomas of the penis

A 10-year-old male with multiple small swellings over the shaft of the penis for 2 years was found to have multiple neurilemmomas on histopathologic examination. The case is reported in view of the extreme rarity of the entity.

Caudal duplication--a case report

Caudal duplication is a rare entity due to incomplete separation of mono-ovular twins. It is usually associated with various congenital malformations involving mainly the genitourinary and gastrointestinal tracts. We report such a case operated upon successfully in which there was no other associated anomaly.

ETS protein-dependent accessibility changes at the immunoglobulin mu heavy chain enhancer

Directed accessibility mediated by antigen-receptor gene enhancers ensures developmental stage-specific activation of V(D)J recombination. Here, we used a combination of in vitro and in vivo assays to explore the mechanisms that regulate immunoglobulin mu heavy chain gene enhancer-dependent chromatin accessibility. Ets-1 or PU.1 bound to mu enhancer-containing plasmids assembled into chromatin in vitro and increased restriction enzyme access to a proximal site. In complementary analyses, expression of PU.1 in Ets-1-containing 2017 pro-T cells or NIH 3T3 cells induced sterile I mu transcripts at the IgH locus and increased accessibility of the endogenous mu enhancer to restriction endonucleases. These observations suggest that one role of PU.1 is to increase accessibility of the mu locus to initiate heavy chain gene expression.

Tolerance and biodegradation of m-toluate by Scots pine, a mycorrhizal fungus and fluorescent pseudomonads individually and under associative conditions

The tolerance to, and degradation of m-toluate by Scots pine (Pinus sylvestris), a symbiotic mycorrhizal fungus (Suillus bovinus) and Pseudomonas fluorescens strains, with or without m-toluate-degrading capacity, was determined individually and in all symbiotic/associative plant-microbe combinations. Fungal survival on medium with m-toluate was increased in co-culture with the degradative bacterial strains on agar plates (up to 0.02%, w/v). When fungi were grown in mycorrhizal association with Scots pine seedlings in test-tube microcosms containing expanded clay pellets and growth media, the fungus was able to withstand m-toluate concentrations up to 2.0%, w/v in all treatments. The seedling tolerance remained unaltered regardless of the presence or absence of mycorrhizal fungi or biodegradative bacteria. Reduction in m-toluate levels was only detected in treatments inoculated with bacterial strains harbouring TOL catabolic plasmids. The plant and fungus, alone or in mycorrhizal symbiosis, were unable to cleave m-toluate. The presence of easily available plant-derived carbon sources did not impede m-toluate degradation by the bacteria in the mycorrhizosphere.

Transcriptional activation by ETS and leucine zipper-containing basic helix-loop-helix proteins

The immunoglobulin mu heavy-chain gene enhancer contains closely juxtaposed binding sites for ETS and leucine zipper-containing basic helix-loop-helix (bHLH-zip) proteins. To understand the mu enhancer function, we have investigated transcription activation by the combination of ETS and bHLH-zip proteins. The bHLH-zip protein TFE3, but not USF, cooperated with the ETS domain proteins PU.1 and Ets-1 to activate a tripartite domain of this enhancer. Deletion mutants were used to identify the domains of the proteins involved. Both TFE3 and USF enhanced Ets-1 DNA binding in vitro by relieving the influence of an autoinhibitory domain in Ets-1 by direct protein-protein associations. Several regions of Ets-1 were found to be necessary, whereas the bHLH-zip domain was sufficient for this effect. Our studies define novel interactions between ETS and bHLH-zip proteins that may regulate combinatorial transcription activation by these protein families.

Presence of pentoxifylline during T cell priming increases clonal frequencies in secondary proliferative responses and inhibits apoptosis

Naive T cells appear to be primed by specific Ag to differentiate into either effectors or memory cells. We have been analyzing the factors involved in this differential commitment in the priming of alloresponsive human T cells in vitro and have shown that the presence of a phosphodiesterase inhibitor, pentoxifylline (POX), during priming results in a decrease in the primary response and enhancement in the secondary proliferative response. We now show that the POX-mediated effect can be mimicked by dibutyryl cAMP. The secondary response enhancement is due to the effects of POX on the T cells rather than the APCs, because even fixed APCs can prime T cells in the presence of POX. POX affects T cells directly by increasing clonal frequency rather than the burst size of the secondary responders. The known inhibition of IL-2 production by POX is not responsible for this effect, because exogenous IL-2 supplementation does not block it. The presence of POX during priming alters the outcome of T cell activation, resulting in a lower frequency of cells expressing IL-2R alpha (CD25) and a decrease in their subsequent apoptosis, and this antiapoptotic effect is consistent with the enhanced commitment of T cells to secondary responsiveness by POX.

A NF-kappa B/c-myc-dependent survival pathway is targeted by corticosteroids in immature thymocytes

Glucocorticoid hormones modulate T cell maturation in vivo. While low levels of hormones are required for appropriate T cell development, high levels of glucocorticoid hormones target immature developing thymocytes for cell death during systemic stress. In this report, we propose a molecular mechanism for the induction of apoptosis in CD4+CD8+ double-positive thymocytes by dexamethasone in vivo. Dexamethasone injection induced the expression of IkappaBalpha and IkappaBbeta in thymocytes and down-regulated NF-kappaB DNA binding activated by intrathymic signals. Down-regulation of NF-kappaB DNA binding preceded cell death, suggesting that NF-kappaB may be important for the survival of immature thymocytes. In addition, ex vivo treatment of thymocyte single-cell suspension with dexamethasone accelerated p65/RelA down-regulation and cell death. Conversely, NF-kappaB induction diminished dexamethasone-induced death. Expression of the c-myc proto-oncogene, a NF-kappaB target, was also reduced in thymocytes of dexamethasone-treated animals, and ectopic transgenic expression of c-myc in mice provided partial rescue of double-positive thymocytes from dexamethasone mediated cell death. These observations suggest that viability of CD4+CD8+ thymocytes may be maintained by an NF-kappaB/c-myc-dependent pathway in vivo.

Exploring functional redundancy in the immunoglobulin mu heavy-chain gene enhancer

Immunoglobulin (Ig) mu heavy-chain gene enhancer activity is mediated by multiple DNA binding proteins. Mutations of several protein binding sites in the enhancer do not affect enhancer activity significantly. This feature, termed redundancy, is thought to be due to functional compensation of the mutated sites by other elements within the enhancer. In this study, we identified the elements that make the basic helix-loop-helix (bHLH) protein binding sites, muE2 and muE3, redundant. The major compensatory element is a binding site for interferon regulatory factors (IRFs) and not one of several other bHLH protein binding sites. These studies also provide the first evidence for a role of IRF proteins in Ig heavy-chain gene expression. In addition, we reconstituted the activity of a monomeric mu enhancer in nonlymphoid cells and defined the domains of the ETS gene required for function.

Induction of premature mitosis in S-blocked onion cells

Onion root-tip cells were blocked at S-phase by treating them with 5-aminouracil (5AU). These cells were then further treated with caffeine/2-aminopurine (Caf/2AP) or a combination of both in the presence of 5AU. These tyrosine kinase inhibitors were able to induce premature mitosis in the S-blocked cells as evident from the breaks and gaps in the metaphase chromosomes and the presence of laggards and fragments in anaphase. Immunofluorescence showed normal spindle formation in these cells. Immunoblotting of cyclin B revealed that the level of cyclin B was slightly higher in the recovered and treated samples than the S-blocked one. The level of p(34)was found to be almost equal in all three samples as expected. We failed to observe any significant difference in the level of p(34)containing phosphorylated tyrosine. Such premature induction of mitosis by the purine derivatives has also been reported in BHK cells. However, those cells failed to progress through mitosis. A comparative analysis indicates that the plant cells and the animal cells, perhaps, follow identical pathway for the initiation of mitosis. The possible causes for differential behaviour in mitotic progression in these cells have been discussed.