Decoupling transcription factor expression and activity enables dimmer switch gene regulation

Gene-regulatory networks achieve complex mappings of inputs to outputs through mechanisms that are poorly understood. We found that in the galactose-responsive pathway in Saccharomyces cerevisiae, the decision to activate the transcription of genes encoding pathway components is controlled independently from the expression level, resulting in behavior resembling that of a mechanical dimmer switch. This was not a direct result of chromatin regulation or combinatorial control at galactose-responsive promoters; rather, this behavior was achieved by hierarchical regulation of the expression and activity of a single transcription factor. Hierarchical regulation is ubiquitous, and thus dimmer switch regulation is likely a key feature of many biological systems. Dimmer switch gene regulation may allow cells to fine-tune their responses to multi-input environments on both physiological and evolutionary time scales.

Bifunctional Small Molecules Enhance Neutrophil Activities Against Aspergillus fumigatus in vivo and in vitro

Aspergillosis is difficult to treat and carries a high mortality rate in immunocompromised patients. Neutrophils play a critical role in control of infection but may be diminished in number and function during immunosuppressive therapies. Here, we measure the effect of three bifunctional small molecules that target Aspergillus fumigatus and prime neutrophils to generate a more effective response against the pathogen. The molecules combine two moieties joined by a chemical linker: a targeting moiety (TM) that binds to the surface of the microbial target, and an effector moiety (EM) that interacts with chemoattractant receptors on human neutrophils. We report that the bifunctional compounds enhance the interactions between primary human neutrophils and A. fumigatus in vitro, using three microfluidic assay platforms. The bifunctional compounds significantly enhance the recruitment of neutrophils, increase hyphae killing by neutrophils in a uniform concentration of drug, and decrease hyphal tip growth velocity in the presence of neutrophils compared to the antifungal targeting moiety alone. We validated that the bifunctional compounds are also effective in vivo, using a zebrafish infection model with neutrophils expressing the appropriate EM receptor. We measured significantly increased phagocytosis of A. fumigatus conidia by neutrophils expressing the EM receptor in the presence of the compounds compared to receptor-negative cells. Finally, we demonstrate that treatment with our lead compound significantly improved the antifungal activity of neutrophils from immunosuppressed patients ex vivo. This type of bifunctional compounds strategy may be utilized to redirect the immune system to destroy fungal, bacterial, and viral pathogens.

Abstract P5-13-03: Fulvestrant plus anastrozole as neoadjuvant therapy in postmenopausal women with hormone receptor positive early breast cancer

Background: Aromatase inhibitors (AIs) are effective in reducing the risk of recurrence from breast cancer (BC) but 20% of patients (pts) with early BC still recur despite adjuvant AIs. Thus more effective endocrine therapies (HTs) are needed. In metastatic BC (MBC), combination of lower dose fulvestrant plus anastrozole improves survival compared to anastrozole alone. The 21-gene Recurrence Score® (RS; Oncotype DX®) has been validated to predict benefit from adding chemotherapy (CT) to HT where pts with a low score have little benefit from CT and derive a large benefit from HT. Ki-67 response to neo-adjuvant HT may predict adjuvant outcomes to HT. Postoperative Endocrine Prognostic Index (PEPI) and modified PEPI may further identify a subset of HT sensitive cancers that do not require adjuvant CT (PEPI 0 category). We conducted a single arm phase II trial to assess the efficacy of fulvestrant plus anastrozole as neoadjuvant HT in pts with operable BC.

Methods: Postmenopausal pts with stage II and III, ER/PR+, HER2 (-) BC with a RS<25 (performed on initial core bx) were included. Duration of neo-adjuvant HT was 4 months. Pts received anastrozole 1mg (PO) daily continuously from day 1 until surgery + fulvestrant (IM) 500mg on day 1, 14 and 28 of cycle 1, and on the last day of three subsequent 28 day cycles (total 6 doses of fulvestrant). At week 4, an optional core bx was repeated to assess change in Ki-67. Response assessments were made clinically every 4 wks. All pts had breast/axillary surgery after the 6th dose of fulvestrant. Ki-67, histologic grade, ER/PR status, and RS were assessed at baseline, core bx at 4 wks, and at definitive surgery. Primary end points were pathologic complete response (pCR) rate and change in Ki-67. Adjuvant CT was left to the discretion of treating physician.

Results: 42 pts were enrolled 7/2009 to 11/2014. Median age was 62. 32 (76%) patients had stage IIA, 7 (17%) had stage IIB and 3 (7%) had stage III disease. 14% had clinically node positive disease. The median RS was 12 (0-24). Median tumor size was 3.5cm. 21%, 74%, and 5% had grade 1, 2 and 3 tumors respectively. Mean ER expression was 95%. 16 (38%) pts had a clinical complete response (cCR), 13 (31%) had a clinical partial response (cPR) and 12 (29%) had stable disease. One pt had progression on therapy. There were no pCRs. Median baseline Ki-67 was 5% (1-36%). 94% of pts had decrease in Ki-67 from baseline to 4-week bx and 97% of pts had decrease in Ki-67 from baseline to surgery. Modified PEPI score at surgery was 0 in 53% of patients. 78% of pts did not receive adjuvant CT. At median follow up of 38 mos only 1 pt had a recurrence with 98% free of a recurrence. There were no grade 3 or grade 4 toxicities.

Conclusions: The neoadjuvant combination of anastrozole and fulvestrant in pts with RS<25 markedly improves Ki-67 response with more than half of pts achieving a modified PEPI score of 0 at surgery. At a relatively short median follow up, recurrence rate is very low. Given the efficacy and tolerability of anastrozole plus fulvestrant in MBC and now in the neo-adjuvant setting, an adjuvant trial of this combination is warranted in pts with ER+ BC.

Citation Format: Khan QJ, Barr JA, Britt AS, Kimler BF, Connor CS, McGinness M, Mammen JMV, Wagner JL, Amin A, Springer M, Baccaray S, Fabian CJ, Sing AP, Sharma P. Fulvestrant plus anastrozole as neoadjuvant therapy in postmenopausal women with hormone receptor positive early breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-13-03.

Abstract OT3-01-12: Phase II trial of lapatinib and everolimus for HER2 positive metastatic breast cancer

Background:

Although the treatment of HER2 positive metastatic breast cancer (MBC) has improved with anti-HER2 agents and chemotherapy, most patients will eventually develop resistance to these agents. Preclinical studies have shown that mTOR inhibition may reverse trastuzumab resistance. We hypothesize that combining mTOR inhibitor everolimus with lapatinib will be an effective strategy for patients who have progressed on prior anti-HER2 therapies.

Trial Design:

We are conducting an open-label phase II pilot study of the combination of everolimus and lapatinib for pts with HER-2 positive MBC. Eligible pts must have histologically documented locally advanced (inoperable) or metastatic HER-2 positive breast cancer that have progressed on at least one HER-2 based regimen in the metastatic or locally advanced setting. Pts with disease progression during or within 12 mos of the completion of adjuvant trastuzumab are eligible. Pts with untreated asymptomatic brain metastases are allowed. Pts with symptomatic brain metastases are allowed to enroll after they have completed radiation and are off steroids. Eligible pts are started on everolimus 5 mg PO daily and lapatinib 1250 mg PO daily without interruption. Among subjects progressing on lapatinib, lapatinib is continued and everolimus initiated. Pts will continue to receive treatment until there is evidence of progressive disease (PD), unacceptable toxicity, or withdrawal of consent. Pts will have radiological evaluation every 8 weeks with CT, bone scan, and MRI brain (for pts with known brain metastasis at baseline).

Specific Aims:

Primary objective is to assess the effectiveness of the combination of RAD-001 and lapatinib as measured by the six-month Overall Response Rate in women with MBC who have progressed on trastuzumab and/or lapatinib based therapies. Secondary objectives are six-month PFS, safety and tolerability of the combination, six-month objective CNS response rate, six-month clinical benefit rate of systemic disease, and six-month clinical benefit rate in CNS.

Statistical methods:

The response rate of lapatinib monotherapy in heavily pre-treated patients is estimated to be 7% (Blackwell 2009). For an expected ORR of 17%, a sample size of 45 subjects will provide 79% power to detect the difference at 0.10 Type I error rate according to 1-sided exact binomial test.

Present accrual and target accrual:

The trial has accrued 20 patients with a target accrual of 45 patients.

Citation Format: Barr JA, Sharma P, Fabian CJ, Yeh H, Baccaray S, Springer M, Khan QJ. Phase II trial of lapatinib and everolimus for HER2 positive metastatic breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr OT3-01-12.

Did you hear the one about the policeman, the doctor and the pharmacist at 30000 feet?

This is the remarkable story of survival against all the odds. A passenger had a myocardial infarction complicated by a witnessed cardiac arrest while on a commercial flight through some of the most remote airspace on the planet. Immediate cardiopulmonary resuscitation and use of an automatic external defibrillator achieved rapid return of spontaneous circulation. Passengers and crew worked effectively together, under the guidance of a physician, to provide critical care to the patient while the flight diverted so he could be transferred to an emergency hospital in Beijing for eventual thrombolysis and postresuscitation care. He made a rapid and full recovery to be discharged from hospital, neurologically intact, 10 days later.

Chemical-specific imaging of shallowly buried objects using femtosecond laser pulses

We demonstrate that objects buried in sand (1 to 4 mm deep) may be selectively imaged according to their chemical composition through spectral analysis of the laser-induced breakdown signal. The signal is generated by loosely focused femtosecond laser pulses having energies ranging from 0.5 to 2.5 mJ. We determine the depth from which a spectral signal may be measured as a function of pulse energy. Having in mind applications to remote sensing, chemical-specific imaging of shallowly buried objects may find use in various fields ranging from space exploration to landmine detection.

Energy transfer between laser filaments in liquid methanol

We demonstrate energy exchange between two filament-forming femtosecond laser beams in liquid methanol. Our results are consistent with those of previous works documenting coupling between filaments in air; in addition, we identify an unreported phenomenon in which the direction of energy exchange oscillates at increments in the relative pulse delay equal to an optical period (2.6 fs). Energy transfer from one filament to another may be used in remote sensing and spectroscopic applications utilizing femtosecond laser filaments in water and air.

Travelers' diarrhea in Nepal: an update on the pathogens and antibiotic resistance

BACKGROUND

Diarrhea is the most common illness among travelers and expatriates in Nepal. Published data on the etiology of travelers' diarrhea (TD) in Nepal are over 13 years old and no prior data exist on antibiotic susceptibility for currently used drugs. We investigated the etiology of diarrhea and antimicrobial susceptibility pattern of bacterial pathogens and compared the results to previous work from the same clinical setting.

METHODS

A total of 381 cases and 176 controls were enrolled between March 2001 and 2003 in a case-control study. Enrollees were over age 18 years from high socioeconomic countries visiting or living in Nepal. Stool samples were assessed by microbiologic, molecular identification, and enzyme immunoassay (EIA) methods, and antimicrobial susceptibility was determined by disk diffusion. Risk factors were assessed by questionnaires.

RESULTS

At least one enteropathogen was identified in 263 of 381 (69%) cases and 47 of 176 (27%) controls (p ≤ 0.001). Pathogens significantly detected among cases were Campylobacter (17%), enterotoxigenic Escherichia coli (ETEC) (15%), Shigella (13%), and Giardia (11%). Cyclospora was detected only in cases (8%) mainly during monsoon season. Although 71% of Campylobacter isolates were resistant to ciprofloxacin, 80% of bacterial isolates overall were sensitive to either ciprofloxacin or azithromycin while 20% were intermediately sensitive or resistant. No bacterial isolates were resistant to both drugs.

CONCLUSIONS

The most common pathogens causing TD in Nepal were Campylobacter, ETEC, and Shigella. Because resistance to fluoroquinolone or azithromycin was similar, one of these drugs could be used as empiric therapy for TD with the other reserved for treatment failures.

The effect of combined application of TGFbeta-1, BMP-2, and COLLOSS E on the development of bone marrow derived osteoblast-like cells in vitro

This study investigated the combined application of Transforming Growth Factor beta-1 (TGFbeta-1) and Bone Morphogenetic Protein-2 (BMP-2) to stimulate osteogenic expression in vitro. TGFbeta-1 and BMP-2 fulfill specific roles in the formation of new bone. COLLOSS E, a bone-derived collagen product containing a variety of naturally occurring growth factors, was also used. Growth factors were administered to osteoblast-like cells from rat bone marrow (RBM). Proliferation and differentiation were monitored up to 24 days, by measuring total DNA content, alkaline phosphatase activity, and calcium content. Genetic expression of a set of differentiation markers at day 7 was measured by Q-PCR. Adding BMP-2 alone induced high proliferation rates, compared to the growth factor supplemented groups, and it induced high differentiation rates, compared to the control group. Adding TGFbeta-1 combined with BMP-2, TGFbeta-1 alone, or COLLOSS E resulted in a significant decrease in proliferation rate, but an increase in differentiation rate, compared to the control group. Additive or synergistic effects of application of TGFbeta-1 and BMP-2 were not observed. The observed effects of COLLOSS E mainly resembled those of TGFbeta-1 application alone. It can be concluded that BMP-2 is the most suitable candidate for osteogenic stimulation of RBM cells in these settings.

Escherichia coli ribosomal protein L20 binds as a single monomer to its own mRNA bearing two potential binding sites

Ribosomal protein L20 is crucial for the assembly of the large ribosomal subunit and represses the translation of its own mRNA. L20 mRNA carries two L20-binding sites, the first folding into a pseudoknot and the second into an imperfect stem and loop. These two sites and the L20-binding site on 23S ribosomal RNA are recognized similarly using a single RNA-binding site located on one face of L20. In this work, using gel filtration and fluorescence cross-correlation spectroscopy (FCCS) experiments, we first exclude the possibility that L20 forms a dimer, which would allow each monomer to bind one site of the mRNA. Secondly we show, using affinity purification and FCCS experiments, that only one molecule of L20 binds to the L20 mRNA despite the presence of two potential binding sites. Thirdly, using RNA chemical probing, we show that the two L20-binding sites are in interaction. This interaction provides an explanation for the single occupancy of the mRNA. The two interacting sites could form a single hybrid site or the binding of L20 to a first site may inhibit binding to the second. Models of regulation compatible with our data are discussed.

Inhibition of human immunodeficiency virus envelope glycoprotein- mediated single cell lysis by low-molecular-weight antagonists of viral entry

The coexpression of human immunodeficiency virus type 1 (HIV-1) envelope glycoproteins and receptors leads to the lysis of single cells by a process that is dependent upon membrane fusion. This cell lysis was inhibited by low-molecular-weight compounds that interfere with receptor binding or with receptor-induced conformational transitions in the envelope glycoproteins. A peptide, T20, potently inhibited cell-cell fusion but had no effect on single cell lysis mediated by the HIV-1 envelope glycoproteins. Thus, critical events in the lysis of single cells by the HIV-1 envelope glycoproteins occur in intracellular compartments accessible only to small inhibitory compounds.

Down-regulation of cell surface CXCR6 expression during T cell activation is predominantly mediated by calcineurin

CXCR6, the receptor for the membrane-anchored chemokine, CXCL16, is expressed on a subset of CCR5-bearing memory T cells, and may play a role in recruiting these cells to sites of inflammation. Here, we set out to determine the effect of T cell activation on CXCR6 expression. Highly purified human peripheral blood T cells were cultured for 7-8 days in presence of IL-2 (400 U/ml) to enhance CXCR6 expression. Overnight stimulation with anti-CD3 mAb+anti-CD28 mAb, which resulted in CD69 induction and cytokine (IL-2 and IFN-gamma) production, reduced cell surface expression of CXCR6 by 85% and that of CCR5 by 76%. The Ca(2+) ionophore, ionomycin (125-500 ng/ml), also markedly diminished CXCR6 expression (85%), but without inducing CD69 expression or cytokine production, and reduced CCR5 expression by only 40%. In contrast, the phorbol esters, PdBu or PMA had little effect on CXCR6 expression (23% reduction) but induced CD69 expression and caused a profound down-regulation (92%) of CCR5 expression. Moreover, CCR7, whose expression was low on CXCR6(+) T cells, was little affected by any of these modes of activation. The down-regulation of CXCR6 expression induced by CD3/CD28 activation was blocked by the broad kinase inhibitor, staurosporine, and by the src kinase inhibitor, PP2, but not by the MEK1 inhibitor, U0106. Most interestingly, the calcineurin inhibitor, FK506, consistently inhibited CD3/CD28-induced CXCR6 down-regulation. FK506 also blocked the decrease of CXCR6 expression caused by ionomycin, whereas staurosporine or PP2 had no effect on this decrease. Altogether, these data indicate that CXCR6 expression is down-regulated, independent of CCR5 or CD69 expression and of cytokine induction, by T cell activation signals that involve predominantly the Ca(2+)-dependent calcineurin pathway.

Marginal adaptation of partial crowns cast in pure titanium and in a gold alloy - an in vivo study

The aim of the present study was to assess in vivo the marginal integrity of partial crowns cast in pure titanium and in a gold alloy. For this purpose, two groups of 25 molars were prepared for partial crowns and then restored with partial crowns cast in Degulor M gold alloy and in pure titanium. At a subsequent session, replicas were produced using a special impression-taking technique. The scanning electron microscope (SEM) technique was used to perform quantitative margin analysis (Tiffmess 1.8 program). The gold alloy partial crowns displayed significantly (P < 0.05) more continuous margin (marginal quality A, <50 microm), and the titanium partial crowns significantly more marginal quality B (50-100 microm) and C (>100 microm). The results show that better marginal integrity can be achieved with gold alloy than with titanium partial crowns. However, in practical terms the difference in marginal quality is only slight, so that the use of pure titanium for single-tooth restorations is justified.

The relationship between translational control and mRNA degradation for the Escherichia coli threonyl-tRNA synthetase gene

Expression of thrS, the gene encoding Escherichia coli threonyl-tRNA synthetase, is negatively autoregulated at the translational level. Regulation is due to the binding of threonyl-tRNA synthetase to its own mRNA at a site called the operator, located immediately upstream of the initiation codon. The present work investigates the relationship between regulation and mRNA degradation. We show that two regulatory mutations, which increase thrS expression, cause an increase in the steady-state mRNA concentration. Unexpectedly, however, the half-life of thrS mRNA in the derepressed mutants is equal to that of the wild-type, indicating that mRNA stability is independent of the repression level. All our results can be explained if one assumes that thrS mRNA is either fully translated or immediately degraded. The immediately degraded RNAs are never detected due to their extremely short half-lives, while the fully translated messengers share the same half-lives, irrespective of the mutations. The increase in the steady-state level of thrS mRNA in the derepressed mutants is simply explained by an increase in the population of translated molecules, i.e. those never bound by the repressor, ThrRS. Despite this peculiarity, thrS mRNA degradation seems to follow the classical degradation pathway. Its stability is increased in a strain defective for RNase E, indicating that an endonucleolytic cleavage by this enzyme is the rate-limiting process in degradation. We also observe an accumulation of small fragments corresponding to the 5' end of the message in a strain defective for polynucleotide phosphorylase, indicating that, following the endonucleolytic cleavages, fragments are normally degraded by 3' to 5' exonucleolytic trimming. Although mRNA degradation was suspected to increase the efficiency of translational control based on several considerations, our results indicate that inhibition of mRNA degradation has no effect on the level of repression by ThrRS.

Strains isogenic to S288C used in the yeast genome sequencing programme carry a functional KSS1 gene

In Saccharomyces cerevisiae, the KSS1 gene encodes the MAP kinase of the invasive/filamentous growth pathway. In addition to its role in this signal transduction pathway, Kssl can replace the Fus3 MAP kinase in the pheromone-response pathway, in the absence of FUS3. Previous work indicated that derivatives of the S288C strain carry a mutant kss1 allele. Here, we report evidence that S288C derivatives used in the Yeast Genome Sequencing Programme carry a functional KSS1 gene and can thus be used to study the regulation of gene expression by KSS1.

Multi-site phosphorylation of Pho4 by the cyclin-CDK Pho80-Pho85 is semi-processive with site preference

As part of a nutrient-responsive signaling pathway, the budding yeast cyclin-CDK complex Pho80-Pho85 phosphorylates the transcription factor Pho4 on five sites and inactivates it. Here, we describe the kinetic reaction between Pho80-Pho85 and Pho4. Through experimentation and computer modeling we have determined that Pho80-Pho85 phosphorylates Pho4 in a semi-processive fashion that results from a balance between kcat and k(off). In addition, we show that Pho80-Pho85 phosphorylates certain sites preferentially. Phosphorylation of the site with the highest preference inhibits the transcriptional activity of Pho4 when it is in the nucleus, while phosphorylation of the lowest-preference sites is required for export of Pho4 from the nucleus. This method of phosphorylation may allow Pho80-Pho85 to quickly inactivate Pho4 in the nucleus and efficiently phosphorylate Pho4 to completion.

An assessment of structured care assistance in the management of patients with type 2 diabetes in general practice

OBJECTIVE

To study differences in diabetes-related parameters in type 2 diabetic patients treated with the support of a Diabetes Service compared to conventional general practice care.

DESIGN

Parallel clinical trial with randomisation at practice level.

SETTING

Fifteen general practices.

PATIENTS

Type 2 diabetic patients, aged < 76 years, treated by a GP.

MAIN OUTCOME MEASURES

Level of glycated haemoglobin (HbA1c).

RESULTS

246 patients entered the study. Final mean HbA1c of all evaluable patients allocated to the intervention (n = 84) was 7.1+/-1.2%, vs 7.5+/-1.8% in the controls (n = 140) (p = 0.06). Patients who were initially poorly controlled (Fasting Blood Glucose > 10 mmol/l) had a significantly lower final HbA1c if they were in an intervention practice (p=0.001). Fewer patients in intervention practices were referred to hospital specialists (1 vs 14).

CONCLUSIONS

Support by the Dutch Diabetes Service did not significantly influence glycated haemoglobin. The subgroup of initially poorly controlled patients developed a significantly lower HbA1c in intervention practices (supported by a Diabetes Service) than in control practices.

Transfer RNA-mediated editing in threonyl-tRNA synthetase. The class II solution to the double discrimination problem

Threonyl-tRNA synthetase, a class II synthetase, uses a unique zinc ion to discriminate against the isosteric valine at the activation step. The crystal structure of the enzyme with an analog of seryl adenylate shows that the noncognate serine cannot be fully discriminated at that step. We show that hydrolysis of the incorrectly formed ser-tRNA(Thr) is performed at a specific site in the N-terminal domain of the enzyme. The present study suggests that both classes of synthetases use effectively the ability of the CCA end of tRNA to switch between a hairpin and a helical conformation for aminoacylation and editing. As a consequence, the editing mechanism of both classes of synthetases can be described as mirror images, as already seen for tRNA binding and amino acid activation.

Effects of screening for disorders among the elderly: an intervention study in general practice

BACKGROUND

Preventive assessment of prevalent disorders may be considered as an instrument to maintain independence in the elderly. However, the outcomes of studies on these types of screening differ considerably regarding their effects.

OBJECTIVES

The aim of the present study was to assess the effects of GPs' screening of the elderly on four highly prevalent disorders with possibilities for treatment: hearing and visual disorders, urinary incontinence and mobility disorders.

METHODS

In an intervention study in 12 general practices, 1121 subjects aged 75 years and over were screened. Randomization was done by practice into an intervention group (576) and a control group (545). In the intervention group, all elderly patients were screened for the four disorders during the first year of the study. When the GP and patient agreed on intervention, usual care was provided by the GP. The patients in the control group were not screened in the first year. In the second year, all patients in both groups were screened for the four disorders.

RESULTS

For none of the four disorders was a measurable effect of the screening at the population level found. In the first year, 1013 new disorders were found involving 479 of 576 people. The GPs considered information to be new in 293 cases. In 245 cases (out of 293), the GP discussed the new information with the patient. Of the 89 cases in which the patient agreed with an intervention, improvement was reported in 17 cases.

CONCLUSIONS

Implementing a standardized screening programme for four highly prevalent disorders for elderly people is not recommended. Preventive assessment of the elderly should be applied in ways other than by screening. Preventive care should pay attention to the individual needs of the elderly, should be started before the age of 75 years and should be offered in a flexible way.

Activation of the Kss1 invasive-filamentous growth pathway induces Ty1 transcription and retrotransposition in Saccharomyces cerevisiae

Using a set of genomic TY1A-lacZ fusions, we show that Ste12 and Tec1, two transcription factors of the Kss1 mitogen-activated protein kinase (MAPK) cascade activate Ty1 transcription in Saccharomyces cerevisiae. This result strongly suggests that the invasive-filamentous pathway regulates Ty1 transcription. Since this pathway is active in diploid cells, we suspected that Ty1 transposition might occur in this cell type, despite the fact that this event has been never reported before (unless activated by heterologous promoters such as that of GAL1). We demonstrate here that constitutive activation of the invasive-filamentous pathway by the STE11-4 allele or by growth in low-nitrogen medium induces Ty1 transcription and retrotransposition in diploid cells. We show that Ty1 retrotransposition can be activated by STE11-4 in haploid cells as well. Our findings provide the first evidence that Ty1 retrotransposition can be activated by environmental signals that affect differentiation. Activation of the Kss1 MAPK cascade by stress is known to cause filament formation that permits the search for nutrients away from the colonization site. We propose that activation of Ty1 retrotransposition by this cascade could play a role in adaptive mutagenesis in response to stress.

Post-transcriptional control by global regulators of gene expression in bacteria

Several authentic or potential global regulators have recently been shown to act at the post-transcriptional level. This is the case for Hfq (HF-1), which is involved in the regulation of an increasing number of genes in Escherichia coli, and CsrA (RsmA) responsible for controlling the expression of genes for extracellular enzymes and secondary metabolism in Gram-negative bacteria. The cold-shock proteins of the CspA family are able to destabilise mRNA secondary structures at low temperature and, therefore, also seem to act post-transcriptionally. These findings illustrate a more general aspect of post-transcriptional control which, in the past, was generally restricted to regulators acting at a single target. The expression of several global transcriptional regulators, such as the stationary phase and heat-shock sigma factors and H-NS, have also recently been shown to be themselves under post-transcriptional control. These examples underline the importance of this type of control in bacterial gene regulation.

Discrimination by Escherichia coli initiation factor IF3 against initiation on non-canonical codons relies on complementarity rules

Translation initiation factor IF3, one of three factors specifically required for translation initiation in Escherichia coli, inhibits initiation on any codon other than the three canonical initiation codons, AUG, GUG, or UUG. This discrimination against initiation on non-canonical codons could be due to either direct recognition of the two last bases of the codon and their cognate bases on the anticodon or to some ability to "feel" codon-anticodon complementarity. To investigate the importance of codon-anticodon complementarity in the discriminatory role of IF3, we constructed a derivative of tRNALeuthat has all the known characteristics of an initiator tRNA except the CAU anticodon. This tRNA is efficiently formylated by methionyl-tRNAfMettransformylase and charged by leucyl-tRNA synthetase irrespective of the sequence of its anticodon. These initiator tRNALeuderivatives (called tRNALI) allow initiation at all the non-canonical codons tested, provided that the complementarity between the codon and the anticodon of the initiator tRNALeuis respected. More remarkably, the discrimination by IF3, normally observed with non-canonical codons, is neutralised if a tRNALIcarrying a complementary anticodon is used for initiation. This suggests that IF3 somehow recognises codon-anticodon complementarity, at least at the second and third position of the codon, rather than some specific bases in either the codon or the anticodon.

Mutations that alter initiation codon discrimination by Escherichia coli initiation factor IF3

This work describes the isolation of mutations in infC, the structural gene for IF3, using different genetic screens. Among 21 mutants characterised, seven were shown to produce stable variant IF3 proteins unable to fully complement a strain carrying a chromosomal deletion of the infC gene. The mutants were also shown to be unable to normally discriminate against several non-canonical initiation codons such as AUU and ACG. The two mutants with the strongest complementation or discrimination defects carry changes in the C-terminal domain of IF3, which is responsible for the binding of the factor to the 30 S ribosomal subunit. We show that the first mutant has an expected decreased but the second an unexpected increased capacity to bind the 30 S subunit. The in vivo defects of the second mutant are explained by its capacity to bind unspecifically to other targets, as shown by its increased affinity for the 50 S subunit, which is normally not recognised by the factor. Interestingly, this mutant corresponds to a change of an acidic residue that might play a negative discriminatory role in preventing interactions with non-cognate RNAs, as has been reported for acidic residues of aminoacyl-tRNA synthetases shown to be involved in tRNA recognition.

The structure of threonyl-tRNA synthetase-tRNA(Thr) complex enlightens its repressor activity and reveals an essential zinc ion in the active site

E. coli threonyl-tRNA synthetase (ThrRS) is a class II enzyme that represses the translation of its own mRNA. We report the crystal structure at 2.9 A resolution of the complex between tRNA(Thr) and ThrRS, whose structural features reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination.

The interdomain linker of Escherichia coli initiation factor IF3: a possible trigger of translation initiation specificity

Initiation factor IF3 is responsible for the accuracy of translation initiation in bacteria, by destabilizing complexes involving non-initiator tRNA and/or nonstart codons. This proofreading is performed on the 30S subunit to which IF3 binds selectively. IF3 has an unusual architecture, with two globular domains connected by a mobile, positively charged linker. Here, we have investigated the function of this flexible tether by probing its conformation when IF3 is bound to the ribosomal RNA. Using site-directed mutagenesis of the linker region, we have also selectively modified its length, its flexibility and its chemical composition. The function of the mutant genes was assayed in vivo, and the structural and biochemical properties of some of the corresponding variant proteins were characterized in vitro. The two isolated domains of IF3 were also co-expressed in order to test the requirement for their covalent attachment. The results indicate that the physical link between the two domains of IF3 is essential for the function of this protein, but that the exact length and chemical composition of the linker can be varied to a large extent. A model is presented in which the extended linker would act as a 'strap', triggering a conformational change in the 30S subunit, which would then ensure initiator tRNA selection.

The phylogenetic position of the musky rat-kangaroo and the evolution of bipedal hopping in kangaroos (Macropodidae: Diprotodontia)

Kangaroos and their relatives (family Macropodidae) are divided into the subfamilies Macropodinae (kangaroos, wallabies, pademelons) and Potoroinae (rat-kangaroos, potoroos, bettongs). The musky rat-kangaroo, Hypsiprymnodon moschatus, is traditionally allied with other potoroines, based primarily on the basis of osteological characters and aspects of the female reproductive system. Unlike other macropodids, however, which are capable of bipedal hopping, Hypsiprymnodon is a quadrupedal bounder and lacks several derived features of the pes and tarsus that are presumably adaptations for bipedal hopping. Other derived features, such as a complex stomach, loss of P2 with the eruption of P3, and reduction of litter size to one, are also lacking in Hypsiprymnodon but occur in all other macropodids. Thus, available evidence suggests that Hypsiprymnodon either is part of a monophyletic Potoroinae or is a sister taxon to other living macropodids. To test these hypotheses, we sequenced 1,170 bp base pairs of the mitochondrial genome for 16 macropodids. Maximum parsimony, minimum evolution, maximum likelihood, and quartet puzzling all support the hypothesis that macropodines and potoroines are united to the exclusion of Hypsiprymnodon. This hypothesis implies that characters such as bipedal hopping evolved only once in macropodid evolution. Aside from Hypsiprymnodon, the remaining macropodids separate into the traditional Macropodinae and Potoroinae. Macropodines further separate into two clades: one containing the New Guinean forest wallabies Dorcopsis and Dorcopsulus, and one consisting of the genera Macropus, Setonix, Thylogale, Onychogalea, Wallabia, Dendrolagus, Peradorcas, and Lagorchestes. Among potoroines, there is moderate support for the association of Bettongia and Aepyprymnus to the exclusion of Potorous. Divergence times were estimated by using 12S ribosomal RNA transversions. At the base of the macropodid radiation, Hypsiprymnodon diverged from other macropodids approximately 45 million years ago. This estimate is comparable to divergence estimates among families of Australasian possums based on single-copy DNA hybridization and 12S rRNA transversions. Macropodines and potoroines, in turn, diverged approximately 30 million years ago. Among macropodines, Dorcopsis and Dorcopsulus separated from other taxa approximately 10 million years ago.

The Escherichia coli threonyl-tRNA synthetase gene contains a split ribosomal binding site interrupted by a hairpin structure that is essential for autoregulation

The expression of the gene encoding Escherichia coli threonyl-tRNA synthetase (ThrRS) is negatively autoregulated at the translational level. ThrRS binds to its own mRNA leader, which consists of four structural and functional domains: the Shine-Dalgarno (SD) sequence and the initiation codon region (domain 1); two upstream hairpins (domains 2 and 4) connected by a single-stranded region (domain 3). Using a combination of in vivo and in vitro approaches, we show here that the ribosome binds to thrS mRNA at two non-contiguous sites: region -12 to +16 comprising the SD sequence and the AUG codon and, unexpectedly, an upstream single-stranded sequence in domain 3. These two regions are brought into close proximity by a 38-nucleotide-long hairpin structure (domain 2). This domain, although adjacent to the 5' edge of the SD sequence, does not inhibit ribosome binding as long as the single-stranded region of domain 3 is present. A stretch of unpaired nucleotides in domain 3, but not a specific sequence, is required for efficient translation. As the repressor and the ribosome bind to interspersed domains, the competition between ThrRS and ribosome for thrS mRNA binding can be explained by steric hindrance.

Evolutionary analyses of the 12-kDa acidic ribosomal P-proteins reveal a distinct protein of higher plant ribosomes

The P-protein complex of eukaryotic ribosomes forms a lateral stalk structure in the active site of the large ribosomal subunit and is thought to assist in the elongation phase of translation by stimulating GTPase activity of elongation factor-2 and removal of deacylated tRNA. The complex in animals, fungi, and protozoans is composed of the acidic phosphoproteins P0 (35 kDa), P1 (11-12 kDa), and P2 (11-12 kDa). Previously we demonstrated by protein purification and microsequencing that ribosomes of maize (Zea mays L.) contain P0, one type of P1, two types of P2, and a distinct P1/P2 type protein designated P3. Here we implemented distance matrices, maximum parsimony, and neighbor-joining analyses to assess the evolutionary relationships between the 12 kDa P-proteins of maize and representative eukaryotic species. The analyses identify P3, found to date only in mono- and dicotyledonous plants, as an evolutionarily distinct P-protein. Plants possess three distinct groups of 12 kDa P-proteins (P1, P2, and P3), whereas animals, fungi, and protozoans possess only two distinct groups (P1 and P2). These findings demonstrate that the P-protein complex has evolved into a highly divergent complex with respect to protein composition despite its critical position within the active site of the ribosome.

Translational coupling by modulation of feedback repression in the IF3 operon of Escherichia coli

A pseudoknot formed by a long-range interaction in the mRNA of the initiation factor 3 (IF3) operon is involved in the translational repression of the gene encoding ribosomal protein L35 by another ribosomal protein, L20. The nucleotides forming the 5' strand of the key stem of the pseudoknot are located within the gene for IF3, whereas those forming the 3' strand are located 280 nt downstream, immediately upstream of the Shine-Dalgarno sequence of the gene for L35. Here we show that premature termination of IF3 translation at a nonsense codon introduced upstream of the pseudoknot results in a substantial enhancement of L20-mediated repression of L35 expression. Conversely, an increase of IF3 translation decreases repression. These results, in addition to an analysis of the effect of mutations in sequences forming the pseudoknot, indicate that IF3 translation decreases L20-mediated repression of L35 expression. We propose that ribosomes translating IF3 disrupt the pseudoknot and thereby attenuate repression. The result is a novel type of translational coupling, where unfolding of the pseudoknot by ribosomes translating IF3 does not increase expression of L35 directly, but alleviates its repression by L20.

The expression of E.coli threonyl-tRNA synthetase is regulated at the translational level by symmetrical operator-repressor interactions

Threonyl-tRNA synthetase from Escherichia coli represses the translation of its own mRNA by binding to the operator region located upstream from the ribosome binding site. The operator contains two stemloop structures which interact specifically with the homodimeric enzyme. Here, we provide in vitro and in vivo evidence that these two stem-loop structures are recognized by the enzyme in an analogous way and mimic the anticodon arm of E.coli tRNA(Thr). Determination of the stoichiometry of the different RNA-threonyl-tRNA synthetase complexes reveals that two tRNA(Thr) molecules bind to the enzyme whereas only one thrS operator interacts with the homodimeric enzyme. A model is presented in which the two anticodon-like domains of the operator bind symmetrically to the two tRNA(Thr) anticodon recognition sites (one per subunit) of the dimeric threonyl-tRNA synthetase. Although symmetrical operator-repressor interactions in transcriptional control are widespread, this report stresses the importance of such interactions in translational regulation of gene expression.

Growth rate-dependent control, feedback regulation and steady-state mRNA levels of the threonyl-tRNA synthetase gene of Escherichia coli

The expression of the gene thrS encoding threonyl-tRNA synthetase is under the control of two apparently different regulatory loops: translational feedback regulation and growth rate-dependent control. The translational feedback regulation is due to the binding of threonyl-tRNA synthetase to a site located in the leader RNA of thrS, upstream of the initiation codon, which mimics the anticodon stem and loop of tRNA(Thr). This binding competes with that of the ribosome and thus inhibits translation initiation. Here, we investigate the mechanism of growth rate-dependent control, i.e. the mechanism by which the synthetase accumulates at high growth rates. We show that growth rate-dependent control acts at the level of translation and requires feedback regulation since mutations that abolish feedback regulation also abolish growth rate-dependent control. We also show that tRNA(Thr), which accumulates at high growth rates, is one of the effectors of growth rate-dependent control since its accumulation can cause derepression independently of growth rate. We show that this tRNA(Thr)-dependent derepression is also dependent on feedback regulation since mutations which abolish feedback also prevent derepression. Based on these results and previous data concerning the mechanism of translational feedback regulation, we propose that threonyl-tRNA synthetase growth rate-dependent control is the consequence of the accumulation at high growth rates of two effectors, the ribosome and tRNA(Thr). We also study the growth rate-dependence of the steady state level of thrS mRNA and show that the steady state level of thrS mRNA increases at high growth rates. This increase is dependent on the translational feedback regulation and can also be detected, independently of growth rate, when thrS mRNA translation is derepressed. Consistently with the model of growth rate-dependent control above, we propose that at high growth rates, the mRNA is well translated and thus stabilised and that, at low growth rates, because of its low translation, thrS mRNA is rapidly degraded.

A long-range RNA-RNA interaction forms a pseudoknot required for translational control of the IF3-L35-L20 ribosomal protein operon in Escherichia coli

In the IF3-L35-L20 operon encoding translation initiation factor 3 (IF3) and the two ribosomal proteins L35 and L20, the expression of the genes that code for the two ribosomal proteins is negatively regulated at the translational level by the cellular concentration of L20. This translational repressor directly regulates the expression of the gene encoding L35 and, via translational coupling, that of its own gene. Mutations that affect the control of the L35 gene were found exclusively at two sites: the first is located approximately 300 nucleotides upstream, and the second immediately 5' of the translation initiation site of the L35 gene. Mutations that fall between these two sites have little or no effect on the control, and the lack of effect of a deletion in the intervening region confirms this finding. RNA structure mapping in vitro suggests that the first site pairs with the second. We show that this pairing is also likely to occur in vivo because single mutations in either of these sites affect control, but base pair compensatory mutations re-establish control. We propose that these two distant sites can base-pair to form a long-range pseudoknot which is required for the control of the expression of the L35 gene.

Depth related distribution of benthic macrofauna in a Costa Rican crater lake

On two different opportunities the distribution and diversity of the benthic macrofauna was studied at different depths in the Laguna del Cerro Chato crater lake, Alajuela, Costa Rica. For both surveys, the deep samples had significantly lower species diversity and evenness than the shallow samples. There was a drop in species diversity and evenness at 6 m, followed by an increase at 9 m. This pattern is associated with fluctuations in the lake's thermocline. Chironomids were the most abundant organism in both surveys and the genus Chironomus dominated at all depths. Analysis of the elements Ca, Cu, S, N, Fe, P and percentage of organic matter in the bottom sediments did not show a clear bathymetrical distribution. However, at a depth of 9 m the increase in both N content and percentage or organic matter could be related to the increase in abundance of organisms.

The role of the AUU initiation codon in the negative feedback regulation of the gene for translation initiation factor IF3 in Escherichia coli

The expression of the infC gene encoding translation initiation factor IF3 is negatively autoregulated at the level of translation, i.e. the expression of the gene is derepressed in a mutant infC background where the IF3 activity is lower than that of the wild type. The special initiation codon of infC, AUU, has previously been shown to be essential for derepression in vivo. In the present work, we provide evidence that the AUU initiation codon causes derepression by itself, because if the initiation codon of the thrS gene, encoding threonyl-tRNA synthetase, is changed from AUG to AUU, its expression is also derepressed in an infC mutant background. The same result was obtained with the rpsO gene encoding ribosomal protein S15. We also show that derepression of infC, thrS, and rpsO is obtained with other 'abnormal' initiation codons such as AUA, AUC, and CUG which initiate with the same low efficiency as AUU, and also with ACG which initiates with an even lower efficiency. Under conditions of IF3 excess, the expression of infC is repressed in the presence of the AUU or other 'abnormal' initiation codons. Under the same conditions and with the same set of 'abnormal' initiation codons, the repression of thrS and rpsO expression is weaker. This result suggests that the infC message has specific features that render its expression particularly sensitive to excess of IF3. We also studied another peculiarity of the infC message, namely the role of a GC-rich sequence located immediately downstream of the initiation codon and conserved through evolution. This sequence was proposed to interact with a conserved region in 16S RNA and enhance translation initiation. Unexpectedly, mutating this GC-rich sequence increases infC expression, indicating that this sequence has no enhancing role. Chemical and enzymatic probing of infC RNA synthesized in vitro indicates that this GC-rich sequence might pair with another region of the mRNA. On the basis of our in vivo results we propose, as suspected from earlier in vitro results, that IF3 regulates the expression of its own gene by using its ability to differentiate between 'normal' and 'abnormal' initiation codons.

Physiological effects of translation initiation factor IF3 and ribosomal protein L20 limitation in Escherichia coli

To investigate the physiological roles of translation initiation factor IF3 and ribosomal protein L20 in Escherichia coli, the infC, rpmI and rpIT genes encoding IF3, L35 and L20, respectively, were placed under the control of lac promotor/operator sequences. Thus, their expression is dependent upon the amount of inducer isopropyl thiogalactoside (IPTG) in the medium. Lysogenic strains were constructed with recombinant lambda phages that express either rpmI and rplT or infC and prmI in trans, thereby allowing depletion of only IF3 or L20 at low IPTG concentrations. At low cellular concentration of IF3, but not L20, decreases and the growth rate slows. Furthermore, ribosomes run off polysomes, indicating that IF3 functions during the initiation phase of protein synthesis in vivo. During slow growth, the ratio of RNA to protein increases rather than decreases as occurs with control strains, indicating that IF3 limitation disrupts feedback inhibition of rRNA synthesis. As IF3 levels drop, expression from an AUU-infC-lacZ fusion increases, whereas expression decreases from an AUG-infC-lacZ fusion, thereby confirming the model of autogenous regulation of infC. The effects of L20 limitation are similar; cells grown in low concentrations of IPTG exhibited a decrease in the rate of growth, a decrease in cellular L20 concentration, no change in IF3 concentration, and a small increase in the ratio of RNA to protein. In addition, a decrease in 50S subunits and the appearance of an aberrant ribosome peak at approximately 41-43S is seen. Previous studies have shown that the L20 protein negatively controls its own gene expression. Reduction of the cellular concentration of L20 derepresses the expression of an rplT-lacZ gene fusion, thus confirming autogenous regulation by L20.

Translational coupling in the Escherichia coli operon encoding translation initiation factor IF3 and ribosomal proteins L20 and L35

The Escherichia coli IF3-L35-L20 operon encodes translation initiation factor IF3 and the ribosomal proteins L35 and L20, respectively. The expression of the genes encoding the two ribosomal proteins is negatively regulated at the translational level by L20, which acts at an operator located within the IF3 gene and just upstream of the L35 gene. We have previously shown that L20 directly represses the expression of the L35 gene, and indirectly that of the L20 gene, via translational coupling. On the basis of mutational analysis and in vitro RNA structure probing experiments, we proposed that a large secondary structure in which the translation initiation site of the L20 gene is sequestered by base-pairing, is responsible for coupling. The ribosome binding site of the L20 gene becomes available when the secondary structure is melted by ribosomes translating the L35 mRNA. Here we describe that this secondary structure forms in vivo by showing that single mutations in either strand reduce coupling and that compensatory mutations that re-establish pairing also re-establish coupling. In vitro 'toeprinting' analysis enabled us to show that the wild-type inhibitory secondary structure directly blocks ribosome binding to the ribosome binding site of rpIT.

Synthetic substrate analogues for UDP-GlcNAc: Man alpha 1-3R beta 1-2-N-acetylglucosaminyltransferase I. Substrate specificity and inhibitors for the enzyme

UDP-GlcNAc:Man alpha 1-3R beta 1-2-N-acetylglucosaminyltransferase I (GlcNAc-T I; EC 2.4.1.101) catalyses the conversion of [Man alpha 1-6(Man alpha 1-3)Man alpha 1-6][Man alpha 1-3]Man beta-O-R to [Man alpha 1-6(Man alpha 1-3)Man alpha 1-6] [GlcNAc beta 1-2Man alpha 1-3]Man beta-O-R (R = 1-4GlcNAc beta 1-4GlcNAc- Asn-X) and thereby controls the conversion of oligomannose to complex and hybrid asparagine-linked glycans (N-glycans). GlcNAc-T I also catalyses the conversion of Man alpha 1-6(Man alpha 1-3)Man beta-O-octyl to Man alpha 1-6(GlcNAc beta 1-2Man alpha 1-3)Man beta-O-octyl. We have therefore tested a series of synthetic analogues of Man"alpha 1-6(Man'alpha 1-3)Man beta-O-octyl as substrates and inhibitors for rat liver GlcNAc-T I. The 2"-deoxy and the 3"-, 4"- and 6"-O-methyl derivatives are all good substrates confirming previous observations that the hydroxyl groups of the Man"alpha 1-6 residue do not play major roles in the binding of substrate to enzyme. In contrasts, all four hydroxyl groups on the Man'alpha 1-3 residue are essential since the corresponding deoxy derivatives either do not bind (2'- and 3'-deoxy) or bind very poorly (4'- and 6'-deoxy) to the enzyme. The 2'- and 3'-O-methyl derivatives also do not bind to the enzyme. However, the 4'-O-methyl derivative is a substrate (KM = 2.6 mM) and the 6'-O-methyl compound is a competitive inhibitor (Ki = 0.76 mM). We have therefore synthesized various 4'- and 6'-O-alkyl derivatives, some with reactive groups attached to an O-pentyl spacer, and tested these compounds as reversible and irreversible inhibitors of GlcNAc-T I. The 6'-O-(5-iodoacetamido-pentyl) compound is a specific time dependent inhibitor of the enzyme. Four other 6'-O-alkyl compounds showed competitive inhibition while the remaining compounds showed little or no binding indicating that the electronic properties of the attached O-pentyl groups influence binding.

Stabilised secondary structure at a ribosomal binding site enhances translational repression in E. coli

The expression of the gene encoding Escherichia coli threonyl-tRNA synthetase is negatively autoregulated at the translational level. The negative feedback is due to the binding of the synthetase to an operator site on its own mRNA located upstream of the initiation codon. The present work describes the characterisation of operator mutants that have the rare property of enhancing repression. These mutations cause (1) a low basal level of expression, (2) a temperature-dependent expression, and (3) an increased capacity of the synthetase to repress its own expression at low temperature. Surprisingly, this enhancement of repression is not explained by an increase of affinity of the mutant operators for the enzyme but by the formation, at low temperature, of a few supplementary base-pairs between the ribosomal binding site and a normally single-stranded domain of the operator. Although this additional base-pairing only slightly inhibits ribosome binding in the absence of repressor, simple thermodynamic considerations indicate that this is sufficient to increase repression. This increase is explained by the competition between the ribosome and repressor for overlapping regions of the mRNA. When the ribosomal binding site is base-paired, the ribosome cannot bind while the repressor can, giving the repressor the advantage in the competition. Thus, the existence of an open versus base-paired equilibrium in a ribosomal binding site of a translational operator amplifies the magnitude of control. This molecular amplification device might be an essential component of translational control considering the low free repressor/ribosome ratio of the low affinity of translational repressors for their target operators.

A novel approach to introduce site-directed specific cross-links within RNA-protein complexes. Application to the Escherichia coli threonyl-tRNA synthetase/translational operator complex

We describe a methodology which allows the introduction of a photoactivatable azido group at specific internal positions of any RNA in order to identify the neighboring elements of an interacting protein. The first step involves site-directed modification of the target RNA with an antisense oligodeoxyribonucleotide bearing, at its 3' or 5' phosphate, a 4-[-N-(2-chloroethyl)-N-methylamino]benzylmethylamino group. Position N7 of a guanine residue located in the close vicinity of the hybrid is the main target for alkylation. The antisense oligodeoxyribonucleotide is then removed by acidic pH treatment and a photoreactive reagent (2,4-dinitro-5-fluorophenylazide) is condensed to the modified nucleotide. This method was used to induce specific cross-links between Escherichia coli threonyl-tRNA synthetase and the leader region of threonyl-tRNA synthetase mRNA, which is involved in translational feedback regulation. Control experiments revealed that the modification affects neither the structure of the mRNA nor the interaction with the enzyme. More than 50% of the modified mRNA complexed with threonyl-tRNA synthetase can be cross-linked to the enzyme, depending on the nucleotide modified.

Synthesis of tetrasaccharide analogues of the N-glycan substrate of beta-(1-->2)-N-acetylglucosaminyltransferase II using trisaccharide precursors and recombinant beta-(1-->2)-N-acetylglucosaminyltransferase I

Recombinant rabbit UDP-GlcNAc: alpha-Man-(1-->3R) beta-(1-->2)-N-acetylglucosaminyl-transferase I (EC 2.4.1.101, GlcNAc-T I) produced in the Sf9 insect cell/baculovirus expression system has been used to convert compounds of the form 3-R-alpha-Man(1-->6)(alpha-Man(1-->3)) beta-Man-O-octyl to 3-R-alpha-Man(1-->6)(beta-GlcNAc(1-->2)alpha-Man(1-->3)) beta-Man-O-octyl where R is OH (14), O-methyl (17), O-pentyl (18), O-(4,4-azo)pentyl (19), O-(5-iodoacetamido)pentyl (20) and O-(5-amino)pentyl (21); 2-deoxy-alpha-Man(1-->6)(beta-GlcNAc(1-->2) alpha-Man(1-->3)) beta-Man-O-octyl (16), 4-O-methyl-alpha-Man(1-->6) (beta-GlcNAc(1-->2) alpha-Man(1-->3)) beta-Man-O-octyl (22), 6-O-methyl-alpha-Man(1-->6)(beta-GlcNAc(1-->2) alpha Man(1-->3)) beta-Man-O-octyl (23) and alpha-Man(1-->6)[beta-GlcNAc(1-->2)(4-O-methyl) alpha-Man(1-->3)] beta-Man-O-octyl (15) were also synthesized by this procedure. The yields ranged from 80 to 99%. Products were characterized by high resolution 1H and 13C nuclear magnetic resonance spectroscopy and fast atom bombardment mass spectrometry. Compounds 14, 15, 17, 22, and 23 are excellent substrates for UDP-GlcNAc: alpha-Man(1-->6R) beta-(1-->2)-N-acetylglucosaminyltransferase II and the other compounds are inhibitors of this enzyme.

Synthetic substrate analogues for UDP-GlcNAc: Man alpha 1-6R beta(1-2)-N-acetylglucosaminyltransferase II. Substrate specificity and inhibitors for the enzyme

UDP-GlcNAc:Man alpha 1-6R beta(1-2)-N-acetylglucosaminyltransferase II (GlcNAc-T II; EC 2.4.1.143) is a key enzyme in the synthesis of complex N-glycans. We have tested a series of synthetic analogues of the substrate Man"'alpha 1-6(GlcNAc"beta 1-2Man'alpha 1-3)Man beta-O-octyl as substrates and inhibitors for rat liver GlcNAc-T II. The enzyme attaches N-acetylglucosamine in beta 1-2 linkage to the 2"'-OH of the Man"'alpha 1-6 residue. The 2"'-deoxy analogue is a competitive inhibitor (Ki = 0.13 mM). The 2"'-O-methyl compound does not bind to the enzyme presumably due to steric hindrance. The 3"'-, 4"'- and 6"'-OH groups are not essential for binding or catalysis since the 3"'-, 4"'- and 6"'-deoxy and -O-methyl derivatives are all good substrates. Increasing the size of the substituent at the 3"'-position to pentyl and substituted pentyl groups causes competitive inhibition (Ki = 1.0-2.5 mM). We have taken advantage of this effect to synthesize two potentially irreversible GlcNAc-T II inhibitors containing a photolabile 3"'-O-(4,4-azo)pentyl group and a 3"'-O-(5-iodoacetamido)pentyl group respectively. The data indicate that none of the hydroxyls of the Man"'alpha 1-6 residue are essential for binding although the 2"'- and 3"'-OH face the catalytic site of the enzyme. The 4-OH group of the Man beta-O-octyl residue is not essential for binding or catalysis since the 4-deoxy derivative is a good substrate; the 4-O-methyl derivative does not bind.(ABSTRACT TRUNCATED AT 250 WORDS)

Translational regulation of the Escherichia coli threonyl-tRNA synthetase gene: structural and functional importance of the thrS operator domains

Previous work showed that E coli threonyl-tRNA synthetase (ThrRS) binds to the leader region of its own mRNA and represses its translation by blocking ribosome binding. The operator consists of four distinct domains, one of them (domain 2) sharing structural analogies with the anticodon arm of the E coli tRNA(Thr). The regulation specificity can be switched by using tRNA identity rules, suggesting that the operator could be recognized by ThrRS as a tRNA-like structure. In the present paper, we investigated the relative contribution of the four domains to the regulation process by using deletions and point mutations. This was achieved by testing the effects of the mutations on RNA conformation (by probing experiments), on ThrRS recognition (by footprinting experiments and measure of the competition with tRNA(Thr) for aminoacylation), on ribosome binding and ribosome/ThrRS competition (by toeprinting experiments). It turns out that: i) the four domains are structurally and functionally independent; ii) domain 2 is essential for regulation and contains the major structural determinants for ThrRS binding; iii) domain 4 is involved in control and ThrRS recognition, but to a lesser degree than domain 2. However, the previously described analogies with the acceptor-like stem are not functionally significant. How it is recognized by ThrRS remains to be resolved; iv) domain 1, which contains the ribosome loading site, is not involved in ThrRS recognition. The binding of ThrRS probably masks the ribosome binding site by steric hindrance and not by direct contacts. This is only achieved when ThrRS interacts with both domains 2 and 4; and v) the unpaired domain 3, which connects domains 2 and 4, is not directly involved in ThrRS recognition. It should serve as an articulation to provide an appropriate spacing between domains 2 and 4. Furthermore, it is possibly involved in ribosome binding.