Maximum entropy determination of mammalian proteome dynamics

Full understanding of proteostasis and energy utilization in cells will require knowledge of the fraction of cell proteins being degraded with different half-lives and their rates of synthesis. We therefore developed a method to determine such information that combines mathematical analysis of protein degradation kinetics obtained in pulse-chase experiments with Bayesian data fitting using the maximum entropy principle. This approach will enable rapid analyses of whole-cell protein dynamics in different cell types, physiological states, and neurodegenerative disease. Using it, we obtained surprising insights about protein stabilities in cultured cells normally and upon activation of proteolysis by mTOR inhibition and increasing cAMP or cGMP. It revealed that >90% of protein content in dividing mammalian cell lines is long-lived, with half-lives of 24 to 200 h, and therefore comprises much of the proteins in daughter cells. The well-studied short-lived proteins (half-lives < 10 h) together comprise <2% of cell protein mass, but surprisingly account for 10 to 20% of measurable newly synthesized protein mass. Evolution thus appears to have minimized intracellular proteolysis except to rapidly eliminate misfolded and regulatory proteins.

Experimental characterization of SiCH+via single-photon ionization of gas-phase SiCH

SiCH and its cation have consistently emerged as predicted species in models of silicon chemistry within the interstellar medium, although they remain unobserved in space. Hindered by their intrinsic instability, no spectroscopic insights have been gleaned concerning the SiCH+ cation. In this study, we present experimental measurements on the SiCH+ cation through single-photon ionization spectroscopy of the SiCH radical within the 8.0-11.0 eV range. Gas-phase SiCH radicals were generated through chemical reactions involving CHx (x = 0-3) and SiHy (y = 0-3) within a microwave discharge flow-tube reactor. Employing a double imaging photoelectron/photoion coincidence spectrometer on the DESIRS beamline at the SOLEIL synchrotron, we recorded mass-selected ion yield and photoelectron spectra. From the analysis of the photoelectron spectrum supported by ab initio calculations and Franck-Condon simulations, the adiabatic ionization energies for the transitions from the X2Π ground electronic state of SiCH toward the X+3Σ- and A+3Π electronic states of SiCH+ have been derived [8.935(6) and 10.664(6) eV, respectively, without spin-orbit correction]. The contribution from the less stable isomer HSiC has been explored in our analysis and ruled out in our experiments.

Single-photon ionization of SiC in the gas phase: experimental and ab initio characterization of SiC. Phys Chem Chem Phys 2023;25:23568-23578. [PMID: 37656136 DOI: 10.1039/d3cp02775a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

We report the first experimental observation of single-photon ionization transitions of the SiC radical between 8.0 and 11.0 eV performed on the DESIRS beamline at the SOLEIL synchrotron facility. The SiC radical, very difficult to synthesize in the gas phase, was produced through chemical reactions between CHx (x = 0-3) and SiHy (y = 0-3) in a continuous microwave discharge flow tube, the CHx and SiHy species being formed by successive hydrogen-atom abstractions induced by fluorine atoms on methane and silane, respectively. Mass-selected ion yield and photoelectron spectra were recorded as a function of photon energy using a double imaging photoelectron/photoion coincidence spectrometer. The photoelectron spectrum enables the first direct experimental determinations of the X+ 4Σ- ← X 3Π and 1+ 2Π ← X 3Π adiabatic ionization energies of SiC (8.978(10) eV and 10.216(24) eV, respectively). Calculated spectra based on Franck-Condon factors are compared with the experimental spectra. These spectra were obtained by solving the rovibrational Hamiltonian, using the potential energy curves calculated at the multireference single and double configuration interaction level with Davidson correction (MRCI + Q) and the aug-cc-pV5Z basis set. MRCI + Q calculations including the core and core-valence electron correlation were performed using the aug-cc-pCV6Z basis set to predict the spectroscopic properties of the six lowest electronic states of SiC+. Complete basis set extrapolations and relativistic energy corrections were also included in the determination of the energy differences characterizing the photoionization process. Using our experimental and theoretical results, we derived semi-experimental values for the five lowest ionization energies of SiC.

Force scaling and efficiency of elongated median fin propulsion

Several fishes swim by undulating a thin and elongated median fin while the body is mostly kept straight, allowing them to perform forward and directional maneuvers. We used a robotic vessel with similar fin propulsion to determine the thrust scaling and efficiency. Using precise force and swimming kinematics measurements with the robotic vessel, the thrust generated by the undulating fin was found to scale with the square of the relative velocity between the free streaming flow and the wave speed. A hydrodynamic efficiency is presented based on propulsive force measurements and modelling of the power required to oscillate the fin laterally. It was found that the propulsive efficiency has a broadly high performance versus swimming speed, with a maximum efficiency of 75%. An expression to calculate the swimming speed over wave speed was found to depend on two parameters:A_p/A_e(ratio between body frontal area to fin swept area) andC_D/C_x(ratio of body drag to fin thrust coefficient). The models used to calculate propulsive force and free-swimming speed were compared with experimental results. The broader impacts of these results are discussed in relation to morphology and the function of undulating fin swimmers. In particular, we suggest that the ratio of fin and body height found in natural swimmers could be due to a trade-off between swimming efficiency and swimming speed.

Threshold photoelectron spectroscopy of 9-methyladenine: theory and experiment

We present a combined experimental and theoretical study of single-photon ionization of 9-methyladenine (9MA) in the gas phase. In addition to tautomerism, several rotamers due to the rotation of the methyl group may exist. Computations show, however, that solely one rotamer contributes because of low population in the molecular beam and/or unfavorable Franck-Condon factors upon ionization. Experimentally, we used VUV radiation available at the DESIRS beamline of the synchrotron radiation facility SOLEIL to record the threshold photoelectron spectrum of this molecule between 8 and 11 eV. This spectrum consists of a well-resolved band assigned mainly to vibronic levels of the D₀ cationic state, plus a contribution from the D₁ state, and two large bands corresponding to the D₁, D₂ and D₃ electronically excited states. The adiabatic ionization energy of 9MA is measured at 8.097 ± 0.005 eV in close agreement with the computed value using the explicitly correlated coupled cluster approach including core valence, scalar relativistic and zero-point vibrational energy corrections. This work sheds light on the complex pattern of the lowest doublet electronic states of 9MA⁺. The comparison to canonical adenine reveals that methylation induces further electronic structure complication that may be important to understand the effects of ionizing radiation and the charge distribution in these biological entities at different time scales.

A new instrument for kinetics and branching ratio studies of gas phase collisional processes at very low temperatures

A new instrument dedicated to the kinetic study of low-temperature gas phase neutral-neutral reactions, including clustering processes, is presented. It combines a supersonic flow reactor with vacuum ultra-violet synchrotron photoionization time-of-flight mass spectrometry. A photoion-photoelectron coincidence detection scheme has been adopted to optimize the particle counting efficiency. The characteristics of the instrument are detailed along with its capabilities illustrated through a few results obtained at low temperatures (<100 K) including a photoionization spectrum of n-butane, the detection of formic acid dimer formation, and the observation of diacetylene molecules formed by the reaction between the C₂H radical and C₂H₂.

Photoionization of C4H5 Isomers

Single-photon, photoelectron-photoion coincidence spectroscopy is used to record the mass-selected ion spectra and slow photoelectron spectra of C₄H₅ radicals produced by the abstraction of hydrogen atoms from three C₄H₆ precursors by fluorine atoms generated by a microwave discharge. Three different C₄H₅ isomers are identified, with the relative abundances depending on the nature of the precursor (1-butyne, 1,2-butadiene, and 1,3-butadiene). The results are compared with our previous work using 2-butyne as a precursor [Hrodmarsson, H. R. J. Phys. Chem. A 2019, 123, 1521-1528]. The slow photoelectron spectra provide new information on the three radical isomers that is in good agreement with previous experimental and theoretical results [Lang, M. J. Phys. Chem. A 2015, 119, 3995-4000; Hansen, N. J. Phys. Chem. A 2006, 110, 3670-3678]. The energy scans of the C₄H₅ photoionization signal are recorded with substantially better resolution and signal-to-noise ratio than those in earlier work, allowing the observation of autoionizing resonances based on excited states of the C₄H₅ cation. Photoelectron images recorded at several energies are also reported, providing insight into the decay processes of these excited states. Finally, in contrast to the earlier work using 2-butyne as a precursor, where H-atom abstraction was the only observed process, F- and H-atom additions to the present precursors are also observed through the detection of C₄H₆F, C₄H₅F, and C₄H₇.

Evidence-based algorithm for the management of acute traumatic retrobulbar haemorrhage

Retrobulbar haemorrhage (RBH) is a potentially blinding consequence of craniofacial trauma, but timely ophthalmic evaluation is difficult to obtain in some settings and clear standards for canthotomy/cantholysis are lacking. We have sought to develop an algorithm to identify vision-threatening traumatic RBH that requires emergent decompression. We retrospectively reviewed 42 consecutive consultations for RBH at a level-one trauma centre. Charts and imaging studies were analysed with attention to mechanism of injury, comorbid trauma, and ophthalmic findings. A total of 22 eyes were observed without intervention, 13 were treated pharmacologically, and seven by emergent canthotomy/cantholysis. No differences in standard trauma metrics were found among these groups. Lid oedema, ecchymosis, chemosis, subconjunctival haemorrhage, and ocular motility also failed to correlate with a need for surgical intervention. "Tight" eyelids (p<0.001), unilateral proptosis (p<0.001), and relative afferent pupillary defect (RAPD; p=0.029), however, all related to a need for canthotomy/cantholysis (Fisher's exact test). Tenting of the globe, which was the only radiographic finding to predict the need for surgery, was seen in just two of the seven cases that required decompression. Many of the traditionally emphasised clinical signs therefore fail to identify cases of RBH that require decompression. Our data support a simple three-factor decision tool. These are: relative proptosis, eyelids that are difficult to open with finger pressure, and presence of an RAPD in the traumatised eye. If all three are noted or if the patient has proptosis and tight lids in the absence of a large preseptal haematoma, he/she is likely to need surgical decompression. Tenting of the globe on computed tomography (CT), while a relatively rare finding, should also alert the physician of the need for intervention.

Study protocol to investigate biomolecular muscle profile as predictors of long-term urinary incontinence in women with gestational diabetes mellitus

BACKGROUND

Pelvic floor muscles (PFM) and rectus abdominis muscles (RAM) of pregnant diabetic rats exhibit atrophy, co-localization of fast and slow fibers and an increased collagen type I/III ratio. However, the role of similar PFM or RAM hyperglycemic-related myopathy in women with gestational diabetes mellitus (GDM) remains poorly investigated. This study aims to assess the frequency of pelvic floor muscle disorders and pregnancy-specific urinary incontinence (PS-UI) 12 months after the Cesarean (C) section in women with GDM. Specifically, differences in PFM/RAM hyperglycemic myopathy will be evaluated.

METHODS

The Diamater is an ongoing cohort study of four groups of 59 pregnant women each from the Perinatal Diabetes Research Centre (PDRC), Botucatu Medical School (FMB)-UNESP (São Paulo State University), Brazil. Diagnosis of GDM and PS-UI will be made at 24-26 weeks, with a follow-up at 34-38 weeks of gestation. Inclusion in the study will occur at the time of C-section, and patients will be followed at 24-48 h, 6 weeks and 6 and 12 months postpartum. Study groups will be classified as (1) GDM plus PS-UI; (2) GDM without PS-UI; (3) Non-GDM plus PS-UI; and (4) Non-GDM without PS-UI. We will analyze relationships between GDM, PS-UI and hyperglycemic myopathy at 12 months after C-section. The mediator variables to be evaluated include digital palpation, vaginal squeeze pressure, 3D pelvic floor ultrasound, and 3D RAM ultrasound. RAM samples obtained during C-section will be analyzed for ex-vivo contractility, morphological, molecular and OMICS profiles to further characterize the hyperglycemic myopathy. Additional variables to be evaluated include maternal age, socioeconomic status, educational level, ethnicity, body mass index, weight gain during pregnancy, quality of glycemic control and insulin therapy.

DISCUSSION

To our knowledge, this will be the first study to provide data on the prevalence of PS-UI and RAM and PFM physical and biomolecular muscle profiles after C-section in mothers with GDM. The longitudinal design allows for the assessment of cause-effect relationships between GDM, PS-UI, and PFMs and RAMs myopathy. The findings may reveal previously undetermined consequences of GDM.

Photoelectron spectroscopy of boron-containing reactive intermediates using synchrotron radiation: BH2, BH, and BF

Mass selected slow photoelectron spectra (SPES) of three boron-containing reactive species, BH₂, BH, and BF were recorded by double imaging photoion-photoelectron coincidence spectroscopy (i²PEPICO) using synchrotron radiation. All species were generated in a flow reactor from the H-abstraction of B₂H₆ by F atoms created in a F₂ microwave discharge. The spectrum of BH₂⁺ exhibits a long bending mode progression with a 970 cm^-1 spacing due to the large geometry change from bent to linear upon ionization. Its ionization energy was determined as 8.12 ± 0.02 eV. For BH, photoionisation from both X¹Σ⁺ singlet and a³Π triplet state was observed, permitting the experimental determination of the singlet/triplet gap (ΔE_ST) from the observed IE's of 9.82 eV and 8.48 eV. In addition, a threshold photoelectron spectrum of BF was recorded, which leads to an IE of 11.11 eV and an improved value for ν_BF⁺ of 1690 cm^-1. All spectra were simulated by calculating Franck-Condon factors from optimised structures based on quantum chemical calculations.

Quantifying Co-Oligomer Formation by α-Synuclein

Small oligomers of the protein α-synuclein (αS) are highly cytotoxic species associated with Parkinson's disease (PD). In addition, αS can form co-aggregates with its mutational variants and with other proteins such as amyloid-β (Aβ) and tau, which are implicated in Alzheimer's disease. The processes of self-oligomerization and co-oligomerization of αS are, however, challenging to study quantitatively. Here, we have utilized single-molecule techniques to measure the equilibrium populations of oligomers formed in vitro by mixtures of wild-type αS with its mutational variants and with Aβ40, Aβ42, and a fragment of tau. Using a statistical mechanical model, we find that co-oligomer formation is generally more favorable than self-oligomer formation at equilibrium. Furthermore, self-oligomers more potently disrupt lipid membranes than do co-oligomers. However, this difference is sometimes outweighed by the greater formation propensity of co-oligomers when multiple proteins coexist. Our results suggest that co-oligomer formation may be important in PD and related neurodegenerative diseases.

Communication: On the first ionization threshold of the C2H radical

The slow photoelectron spectrum of the ethynyl radical has been recorded for the first time by using the DESIRS beamline of the SOLEIL synchrotron facility. Ethynyl was generated using a microwave discharge flow tube. The observation of the X⁺Π3←XΣ+2 transition allowed the first direct measurement of the adiabatic ionization threshold of this radical (E_I = 11.641(5) eV). The experimental results are supported by ab initio calculations. Our preliminary investigation of the cationic ground state potential energy surfaces predicts a non-negligible Renner-Teller effect which has not been discussed previously.

Quantitative analysis of co-oligomer formation by amyloid-beta peptide isoforms

Multiple isoforms of aggregation-prone proteins are present under physiological conditions and have the propensity to assemble into co-oligomers with different properties from self-oligomers, but this process has not been quantitatively studied to date. We have investigated the amyloid-β (Aβ) peptide, associated with Alzheimer’s disease, and the aggregation of its two major isoforms, Aβ40 and Aβ42, using a statistical mechanical modelling approach in combination with in vitro single-molecule fluorescence measurements. We find that at low concentrations of Aβ, corresponding to its physiological abundance, there is little free energy penalty in forming co-oligomers, suggesting that the formation of both self-oligomers and co-oligomers is possible under these conditions. Our model is used to predict the oligomer concentration and size at physiological concentrations of Aβ and suggests the mechanisms by which the ratio of Aβ42 to Aβ40 can affect cell toxicity. An increased ratio of Aβ42 to Aβ40 raises the fraction of oligomers containing Aβ42, which can increase the hydrophobicity of the oligomers and thus promote deleterious binding to the cell membrane and increase neuronal damage. Our results suggest that co-oligomers are a common form of aggregate when Aβ isoforms are present in solution and may potentially play a significant role in Alzheimer’s disease.

Asymptotic solutions of the Oosawa model for the length distribution of biofilaments

Nucleated polymerisation phenomena are general linear growth processes that underlie the formation of a range of biofilaments in nature, including actin and tubulin that are key components of the cellular cytoskeleton. The conventional theoretical framework for describing this process is the Oosawa model that takes into account homogeneous nucleation coupled to linear growth. In his original work, Oosawa provided an analytical solution to the total mass concentration of filaments; the time evolution of the full length distribution has, however, been challenging to access, in large part due to the nonlinear nature of the rate equations inherent in the description of such phenomena and to date analytical solutions for the filament distribution are known only in certain special cases. Here, by exploiting a technique based on the method of matched asymptotics, we present an analytical treatment of the Oosawa model that describes the shape of the length distribution of biofilaments reversibly growing through primary nucleation and filament elongation. Our work highlights the power of matched asymptotics for obtaining closed-form analytical solutions to nonlinear master equations in biophysics and allows us to identify the key time scales that characterize biological polymerization processes.

Nucleation-conversion-polymerization reactions of biological macromolecules with prenucleation clusters

The self-assembly of biomolecules, such as peptides and proteins, into filaments is conventionally understood as a nucleated polymerization reaction. However, detailed analysis of experimental observation has revealed recently that nucleation pathways generate growth-competent nuclei via a cascade of metastable intermediate species, which are omitted in conventional models of filamentous growth based on classical nucleation theory. Here we take an analytical approach to generalizing the classical theory of nucleated polymerization to include the formation of these prenucleation clusters, providing a quantitative general classification of the behavior exhibited by these nucleation-conversion-polymerization reactions. A phase diagram is constructed, and analytical predictions are derived for key experimental observables. Using this approach, we delineate the characteristic time scales that determine the nature of biopolymer growth phenomena.

Isotopically resolved photoelectron imaging unravels complex atomic autoionization dynamics by two-color resonant ionization

Angle-resolved electron spectroscopy in coincidence with high-resolution mass spectroscopy has been applied to study two-color resonant photoionization in atomic xenon. Separation of different isotopes enabled us to extract results for the electronic dynamics free from depolarization effects, which are generally introduced by the coupling of the electronic and nuclear angular momenta. The concerted experimental and theoretical analysis of the photoelectron angular distributions in the region of an autoionizing resonance emphasizes the strong sensitivity of the observed structures to the fine details of the treatment of the underlying dynamics.

DELICIOUS III: a multipurpose double imaging particle coincidence spectrometer for gas phase vacuum ultraviolet photodynamics studies

We present a versatile double imaging particle coincidence spectrometer operating in fully continuous mode, named DELICIOUS III, which combines a velocity map imaging device and a modified Wiley-McLaren time of flight momentum imaging analyzer for photoelectrons and photoions, respectively. The spectrometer is installed in a permanent endstation on the DESIRS vacuum ultraviolet (VUV) beamline at the French National Synchrotron Radiation Facility SOLEIL, and is dedicated to gas phase VUV spectroscopy, photoionization, and molecular dynamics studies. DELICIOUS III is capable of recording mass-selected threshold photoelectron photoion coincidence spectra with a sub-meV resolution, and the addition of a magnifying lens inside the electron drift tube provides a sizeable improvement of the electron threshold/ion mass resolution compromise. In fast electron mode the ultimate kinetic energy resolution has been measured at ΔE/E = 4%. The ion spectrometer offers a mass resolution--full separation of adjacent masses--of 250 amu for moderate extraction fields and the addition of an electrostatic lens in the second acceleration region allows measuring the full 3D velocity vector for a given mass with an ultimate energy resolution of ΔE/E = 15%, without sacrificing the mass resolution. Hence, photoelectron images are correlated both to the mass and to the ion kinetic energy and recoil direction, to access the electron spectroscopy of size-selected species, to study the photodissociation processes of state-selected cations in detail, or to measure in certain cases photoelectron angular distributions in the ion recoil frame. The performances of DELICIOUS III are explored through several examples including the photoionization of N2, NO, and CF3.

sEMG-based detection of poor posture: a feasibility study

The cost of the medical treatment of low back pain (LBP) was estimated to be $24 billion in the early 90s. Also, 80% of the LBP is estimated to be due to poor or inappropriate posture. The ultimate goal of the project is to develop a surface electromyography (sEMG)-based device that could be used to prevent and treat LBP by postural re-education or simply for on-the-spot sEMG feedback. In this paper we present the results and conclusions of a feasibility study for sEMG-based poor posture classifier. The results show that a s-EMG based poor posture classifier could be possible. The sensitivity for the best linear classifier model was 72% and the specificity was 78%. The same signal feature returned very different results from one participant to another. This inter-subject variability could be due to different muscular activation patterns during posture correction.

State-selected unimolecular decomposition of δ-valerolactam+ and δ-valerolactam2+ cations: theory and experiment

The near threshold photofragmentation pattern of δ-valerolactam(+) and δ-valerolactam(2)(+) has been recorded combining electron/ion coincidence techniques and vacuum ultraviolet synchrotron radiation. The experimental method yields the fragment intensity as a function of the internal energy deposited into the parent cation, up to 3.1 eV above the first ionization threshold. In parallel, ab initio studies on the δ-valerolactam(+) and δ-valerolactam(2)(+) cations and their ionic and neutral fragmentation products have been performed with the aim of determining the isomers of the ionic products observed experimentally as well as of their neutral counterparts. These computations were performed using the PBE0 exchange-correlation functional and the aug-cc-pVDZ basis set. We found good agreement between the calculated reaction enthalpies and experimental appearance energies of the ions. More generally, our experimental and theoretical results reveal that the fragmentation of the ionic species of interest leads to a multitude of neutral and ionic fragments, which may be formed after intramolecular isomerization and complex decomposition processes. Multistep reaction pathways are expected.

Maxi program at IEEE EMBS Student Club of Beijing University of Posts and Telecommunications

This paper presents the recently launched Maxi Program at IEEE EMBS Student Club of Beijing University of Posts and Telecommunications. The program initiates a variety of seminar series covering biomedical expertise and professional communication skills, forms a cooperative partnership between students, university and industry through guest speakers events and industry tours, and sets in motion personal consultative services (PCS) to foster the individualized competence of students. This extended program could be an innovative model of self-development as an affiliated student chapter/club with IEEE EMBS.

Effect of norethisterone and its A-ring reduced metabolites on the acrosome reaction in porcine spermatozoa

The synthetic progestin, norethisterone (NET), has been reported as a contragestational postcoital agent in humans, rodents and rabbits. The effect and molecular mechanisms of NET and its A-ring reduced metabolites, 5alpha-NET and 3beta5alpha-NET, on the acrosome reaction (AR) are unknown. The aim of this study was to assess the effect of these compounds on an in vitro progesterone-induced AR in porcine spermatozoa. The spermatozoa were obtained from semen ejaculated by proven fertile adult pigs. Seminal plasma removed and incubated under capacitating conditions was performed in TALP-Hepes medium for 4 h. Progesterone (P4) and three different progestins: norethisterone (NET), 5alpha-norethisterone (5alpha-NET) and 3beta5alpha-NET were then added at equimolar doses, and the spermatozoa were incubated for 15 min. Double-staining with PSA-FITC and Hoechst-33258 assessed the AR and sperm viability. Both P4 and NET induced the AR, while 5alpha-NET not only did not induce this process, but was able to block the effect of P4 on the spermatozoa. 3beta5alpha-NET was not able to inhibit P4 action. These results suggest that NET and its A-ring reduced metabolites act in different ways on the progesterone-induced AR in porcine spermatozoa.

tRNA-guanine transglycosylase from Escherichia coli: molecular mechanism and role of aspartate 89

The enzyme tRNA-guanine transglycosylase (TGT, EC 2.4.2.29) catalyzes a posttranscriptional transglycosylation reaction involved in the incorporation of the modified base queuine [Q, 7-(4,5-cis-dihydroxy-2-cyclopenten-1-ylaminomethyl)-7-deazaguanine] into tRNA. Previously, the crystal structure of the TGT from Zymomonas mobilis was solved in complex with preQ(1) (the substrate for the eubacterial TGT) [Romier et al. (1996) EMBO J. 15, 2850-2857]. An aspartate residue at position 102 (position 89 in the Escherichia coli TGT) was proposed to play a nucleophilic role in an associative catalytic mechanism. Although this is an attractive and precedented mechanism, a dissociative mechanism is equally plausible. In a dissociative mechanism, aspartate 89 would provide electrostatic stabilization of an oxocarbenium ion intermediate that is formed by dissociation of guanine. To clarify the nature of the catalytic mechanism of TGT, we have generated and characterized four mutations of aspartate 89 in the E. coli TGT (alanine, asparagine, cysteine, and glutamate). All four mutant TGTs were able to noncovalently bind tRNA, but only the glutamate mutant was able to form a stable complex with the RNA substrate under denaturing conditions that was comparable to wild type. Furthermore, the glutamate mutant was the only mutant TGT that demonstrated significant activity. Kinetic parameters were determined for this enzyme and shown to be comparable to wild type, revealing that the enzyme is considerably tolerant of the positioning of the carboxylate. Under conditions of high enzyme concentrations and long time courses, the alanine, asparagine, and cysteine mutants showed very low levels (ca. 10(3)-fold lower than wild type) of activity that were linear with respect to enzyme concentration and dependent upon pH in a fashion similar to that of the wild type. However, the observed initial velocities were too low to accurately determine k(cat) and K(m) values. We hypothesize that the activity observed for these mutants is most likely derived from host strain TGT (wt) contamination. These results are most consistent with aspartate 89 acting as a nucleophile in an associative catalytic mechanism.

tRNA recognition by tRNA-guanine transglycosylase from Escherichia coli: the role of U33 in U-G-U sequence recognition

In eubacteria, the biosynthesis of queuine, a modified base found in the wobble position (#34) of tRNAs coding for Tyr, His, Asp, and Asn, occurs via a multistep pathway. One of the key enzymes in this pathway, tRNA-guanine transglycosylase (TGT), exchanges the genetically encoded guanine at position 34 with a queuine precursor, preQ1. Previous studies have identified a minimal positive RNA recognition motif for Escherichia coli TGT consisting of a stable minihelix that contains a U-G-U sequence starting at the second position of its seven base anticodon loop. Recently, we reported that TGT was capable of recognizing the U-G-U sequence outside of this limited structural context. To further characterize the ability of TGT to recognize the U-G-U sequence in alternate contexts, we constructed mutants of the previously characterized E. coli tRNA(Tyr) minihelix. The U-G-U sequence was shifted to various positions within the anticodon loop of these mutants. Characterization of these analogs demonstrates that in addition to the normal U33G34U35 position, TGT can also recognize the U34G35U36 analog (UGU(+1)). The other analogs were not active. This indicates that the recognition of the U-G-U sequence is not strictly dependent upon its position relative to the stem. In E. coli, the full-length tRNA with a U34G35U36 anticodon sequence is one of the isoacceptors that codes for threonine. We found that TGT is able to recognize tRNA(Thr(UGU)) but only in the absence of a uridine at position 33. U33, an invariant base present in all tRNAs, has been shown to strongly influence the conformation of the anticodon loop of certain tRNAs. We find that mutation of this base confers on TGT the ability to recognize U34G35U36, and suggests that loop conformation affects recognition. The fact that the other analogs were not active indicates that although TGT is capable of recognizing the U-G-U sequence in additional contexts, this recognition is not indiscriminate.

A new target for shigellosis: rational design and crystallographic studies of inhibitors of tRNA-guanine transglycosylase

Eubacterial tRNA-guanine transglycosylase (TGT) is involved in the hyper-modification of cognate tRNAs leading to the exchange of G34 at the wobble position in the anticodon loop by preQ1 (2-amino-5-(aminomethyl)pyrrolo[2,3-d]pyrimidin-4(3H)-one) as part of the biosynthesis of queuine (Q). Mutation of the tgt gene in Shigella flexneri results in a significant loss of pathogenicity of the bacterium, revealing TGT as a new target for the design of potent drugs against Shigellosis. The X-ray structure of Zymomonas mobilis TGT in complex with preQ1 was used to search for new putative inhibitors with the computer program LUDI. An initial screen of the Available Chemical Directory, a database compiled from commercially available compounds, suggested several hits. Of these, 4-aminophthalhydrazide (APH) showed an inhibition constant in the low micromolar range. The 1.95 A crystal structure of APH in complex with Z. mobilis TGT served as a starting point for further modification of this initial lead.

tRNA-guanine transglycosylase from Escherichia coli: recognition of noncognate-cognate chimeric tRNA and discovery of a novel recognition site within the TpsiC arm of tRNA(Phe)

tRNA-guanine transglycosylase (TGT) is a key enzyme involved in the posttranscriptional modification of tRNA across the three kingdoms of life. In eukaryotes and eubacteria, TGT is involved in the introduction of queuine into the anticodon of the cognate tRNAs. In archaebacteria, TGT is responsible for the introduction of archaeosine into the D-loop of the appropriate tRNAs. The tRNA recognition patterns for the eubacterial (Escherichia coli) TGT have been studied. These studies are all consistent with a restricted recognition motif involving a U-G-U sequence in a seven-base loop at the end of a helix. While attempting to investigate the potential of negative recognition elements in noncognate tRNAs via the use of chimeric tRNAs, we have discovered a second recognition site for the E. coli TGT in the TpsiC arm of in vitro-transcribed yeast tRNA(Phe). Kinetic analyses of synthetic mutant oligoribonucleotides corresponding to the TpsiC arm of the yeast tRNA(Phe) indicate that the specific site of TGT action is G53 (within a U-G-U sequence at the transition of the TpsiC stem into the loop). Posttranscriptional base modifications in tRNA(Phe) block recognition by TGT, most likely due to a stabilization of the tRNA structure such that G53 is inaccessible to TGT. These results demonstrate that TGT can recognize the U-G-U sequence within a structural context that is different than the canonical U-G-U in the anticodon loop of tRNA(Asp). Although it is unclear if this second recognition site is physiologically relevant, this does suggest that other RNA species could serve as substrates for TGT in vivo.

Mutagenesis and crystallographic studies of Zymomonas mobilis tRNA-guanine transglycosylase to elucidate the role of serine 103 for enzymatic activity

The tRNA modifying enzyme tRNA-guanine transglycosylase (TGT) is involved in the exchange of guanine in the first position of the anticodon with preQ1 as part of the biosynthesis of the hypermodified base queuine (Q). Mutation of Ser90 to an alanine in Escherichia coli TGT leads to a dramatic reduction of enzymatic activity (Reuter, K. et al. (1994) Biochemistry 33, 7041-7046). To further clarify the role of this residue in the catalytic center, we have mutated the corresponding Ser103 of the crystallizable Zymomonas mobilis TGT into alanine. The crystal structure of a TGT(S103A)/preQ1 complex combined with biochemical data presented in this paper suggest that Ser103 is essential for substrate orientation in the TGT reaction.

The androgenic effect of norethisterone and 5alpha-norethisterone on the contractile response of the rat vas deferens to methoxamine and serotonin

Norethisterone (NET) and its metabolite 5alpha-norethisterone (5alpha-NET) are competitors for the androgen receptor. The sensitivity of the rat vas deferens to the contractile action of methoxamine and serotonin is regulated by hormonal and anatomical factors. The aim of this study was to evaluate the ability of NET and 5alpha-NET to induce the androgen-regulated contractile response to methoxamine and serotonin in the epididymal and prostatic portions of rat vas deferens. Adult male rats either intact, castrated or steroid-treated castrated were used. The contractility was recorded isometrically, and non-cumulative concentration-response curves to either methoxamine or serotonin were obtained. NET and 5alpha-NET partially restored the sensitivity to methoxamine and serotonin in the epididymal portion of castrated rats. The maximal responses to both agonists were significantly higher than those observed in castrated rats, and significantly lower than the responses observed in either intact or androgen-treated castrated rats. The prostatic portion was less responsive to both agonists than the epididymal portion, in all groups but castrated rats, as castration induced sensitivity to both agonists. NET and 5alpha-NET displayed a partial though similar androgenic activity in the rat vas deferens. These results contrast with previous reports where a decrease of androgenic effect due to the 5alpha-reduction of NET has been found.

tRNA-guanine transglycosylase from Escherichia coli: recognition of full-length 'queuine-cognate' tRNAs

A key enzyme involved in the incorporation of the modified base queuine into tRNA (position 34) is tRNA-guanine transglycosylase (TGT). Studies of the recognition of truncated tRNAs by the Escherichia coli TGT have established a minimal recognition motif involving a minihelix with a 7 base loop containing a U-G-U sequence (where G is replaced with queuine) [Curnow, A.W. and Garcia, G.A. (1995) J. Biol. Chem. 270, 17264-17267; Nakanishi, S. et al. (1994) J. Biol. Chem. 269, 32221-32225]. Still, a clearer understanding of the recognition of full-length 'queuine-cognate' tRNAs by TGT remains lacking. In this paper, we report the in vitro transcription and enzymological characterization (Km, and kcat) of all four 'queuine-cognate' tRNAs from E. coli and from Saccharomyces cerevisiae with the TGT from E. coli. No primary or secondary structures emerge as important recognition elements from this study. The modest differences in substrate specificity (relative kcat/Km values vary from 0.5 to 8.4) seen among these 'queuine-cognate' tRNAs most likely result from the accumulated effects of many subtle factors. Interestingly, the yeast tRNAs are essentially equivalent to the E. coli tRNAs as substrates for TGT, indicating that there is nothing intrinsic to the yeast tRNAs that accounts for the absence of queuine in yeast.

Vitreous body glutamate concentration in dogs with glaucoma

OBJECTIVE

To analyze the vitreal amino acid concentrations in dogs with breed-related primary glaucoma to determine whether excitotoxic amino acids associated with retinal genglion cell death in other species were present in affected dogs.

SAMPLES

11 normal control and 10 glaucomatous canine eyes.

PROCEDURE

Amino acid analyses were performed by high-pressure liquid chromatography in masked manner.

RESULTS

Eyes from dogs with primary glaucoma had significantly high vitreal glutamate concentration, compared with values for eyes of clinically normal control dogs. Mean (+/-SD) glutamate concentrations were 31.7 +/- 12.4 and 6.9 +/- 6.3 microM in glaucomatous and normal eyes, respectively (P < 0.0001). Eyes from dogs with glaucoma also had lower vitreal glycine (37.0 +/- 17.0 vs 59.4 +/- 28.2 microM; P < 0.043) and higher of vitreal tryptophan (39.0 +/- 22.8 vs 17.5 +/- 11.2 microM; P < 0.012) concentrations, compared with values for normal eyes.

CONCLUSION

Glutamate concentration potentially toxic to retinal ganglion cells is associated with the pathogenesis of primary glaucoma in dogs. Increased glutamate concentration provides evidence of an ischemic mechanism for retinal ganglion cell death and optic nerve atrophy in dogs with glaucoma.

CLINICAL RELEVANCE

The emphasis on reduction and normalization of high intraocular pressure as the primary focus of treatment for glaucoma in dogs should be augmented by other therapeutic approaches.

Cysteine 265 is in the active site of, but is not essential for catalysis by tRNA-guanine transglycosylase (TGT) from Escherichia coli

Site-directed mutagenesis and X-ray absorption spectroscopy studies have previously shown that the tRNA-guanine transglycosylase (TGT) from Escherichia coli is a zinc metalloprotein and identified the enzymic ligands to the zinc [Chong et al. (1995), Biochemistry 34, 3694-3701; Garcia et al. (1966), Biochemistry 35, 3133-3139]. During these studies one mutant, TGT (C265A), was found to exhibit a significantly lower specific activity, but was not found to be involved in the zinc site. The present report demonstrates that TGT is inactivated by treatment with thiol reagents (e.g., DTNB, MMTS, and N-ethylmaleimide). Further, this inactivation is shown to be due to modification of cysteine 265. The kinetic parameters for the mutants TGT (C265A) and TGT (C265S), however, suggest that this residue is not performing a critical role in the TGT reaction. We conclude that cysteine 265 is in the active site of TGT, but is not performing a critical catalytic function. This conclusion is supported by the recent determination of the X-ray crystal structure of the TGT from Zymomonas mobilis [Romier et al. (1966), EMBO J. 15, 2850-2857], which reveals that the residue corresponding to cysteine 265 is distant from the putative catalytic site, but is in the middle of a region of the enzyme surface proposed to bind tRNA.

X-ray absorption spectroscopy of the zinc site in tRNA-guanine transglycosylase from Escherichia coli

A key step in the post-transcriptional modification of tRNA with queuine in Escherichia coli is the exchange of the queuine precursor, preQ1 into tRNA. This reaction is catalyzed by tRNA-guanine transglycosylase (TGT). We have previously shown that the E. coli TGT is a zinc metalloprotein [Chong et al. (1995) Biochemistry 34, 3694-3701]. Site-directed mutagenesis studies indicated that cysteines 302, 304, 307 and histidine 317 constitute the four ligands to the zinc. The involvement of histidine 317 is somewhat confounded by the presence of histidine 316. We have examined the zinc site in TGT (wt) and TGT (H317C) by X-ray absorption spectroscopy. The TGT (wt) data are most consistent with a tetracoordinate zinc with one nitrogen and three sulfur ligands. Interestingly, the data for TGT (H317C) are also consistent with a tetracoordinate zinc with one nitrogen and three sulfur ligands. The outer shell imidazole scattering for TGT (H317C) appears to be somewhat more ordered than that for TGT (wt), consistent with our previous suggestion that the wild-type enzyme may exist in two conformations the predominant one involving histidine 317 liganding to the zinc and the minor conformer involving histidine 316 liganding to the zinc. The minor conformer, with histidine 316 coordinating the zinc, appears to have an overall conformation that is subtly different from that of the wild-type enzyme. While TGT (H317C) has kinetic parameters very similar to the wild-type, it does not form the homotrimer quaternary structure of the wild-type. TGT (H317A) has previously [Chong et al. (1995) Biochemistry 34, 3694-3701] been found to contain a significant amount of zinc, but is essentially inactive. This suggests that careful analysis of EXAFS data can reveal subtle conformational changes in metal binding sites that are not observed in more common probes of protein conformation such as CD spectroscopy.

Mechanism-based inactivation of tRNA-guanine transglycosylase from Escherichia coli by 2-amino-5-(fluoromethyl)pyrrolo[2,3-d]pyrimidin-4 (3H)-one

In Escherichia coli, tRNA-guanine transglycosylase (TGT) catalyzes the incorporation of the queuine precursor preQ1 [2-amino-5-(aminomethyl)pyrrolo[2,3-d]pyrimidin-4(3H)-one] into tRNA. This precursor is further elaborated to queuine by two subsequent enzymic reactions [Slany, R. K., & Kersten, H. (1994) Biochimie 76, 1178-1182]. Our previous studies [Hoops, G. C., Townsend, L. B., & Garcia, G. A., (1995) Biochemistry (in press)] on a series of synthetic 5- and 6-substituted 2-aminopyrrolo[2,3-d]pyrimidin-4(3H) -ones have revealed that the E. coli TGT tolerates a wide diversity of substituents (isosteric, or nearly so, to the aminomethyl group of preQ1) at the 5 position. We report here that 2-amino-5-(fluoromethyl)pyrrolo[2,3-d]pyrimidin-4 (3H)-one (FMPP) inactivates TGT in a time- and concentration-dependent manner with k(inact) = 0.074 min-1 and KI = 136 microM. A competitive inhibitor (7-methyl-preQ1), with respect to preQ1, of TGT [Hoops, G.C., Townsend, L.B., & Garcia, G.A. (1995) Biochemistry (in press)] protects the enzyme from inactivation by FMPP. FMPP also acts as a competitive inhibitor (KI = 114 microM) of TGT under initial velocity conditions. The rate of fluoride release from FMPP is slightly faster (0.064 min-1) than the k(inact) (0.053 min-1) at 300 microM FMPP, consistent with fluoride release preceding inactivation. FMPP appears to partition between "normal" turnover (kcat = 0.461 min-1 and Km = 152 microM), inactivation, and an alternative processing to an unidentified, fluoride-released product.(ABSTRACT TRUNCATED AT 250 WORDS)

tRNA-guanine transglycosylase from Escherichia coli: structure-activity studies investigating the role of the aminomethyl substituent of the heterocyclic substrate PreQ1

A series of 5-substituted 2-aminopyrrolo[2,3-d]pyrimidin-4(3H)-ones have been synthesized in order to study the substrate specificity of the tRNA-guanine transglycosylase (TGT) from Escherichia coli. A number of these compounds were initially examined as inhibitors of radiolabeled guanine incorporation into tRNA catalyzed by TGT [Hoops, G. C., Garcia, G. A., & Townsend, L. B. (1992) 204th National Meeting of the American Chemical Society, Washington, DC, August 23-28, 1992, Division of Medicinal Chemistry, Abstract 113]. The kinetic parameters of these analogues as substrates in the TGT reaction have been determined by monitoring the loss of radiolabeled guanine from 8-[14C]G34-tRNA. This study reveals that the tRNA-guanine transglycosylase from E. coli will tolerate a wide variety of substituents at the 5-position. The role of the 5-substituent appears to be entirely in binding/recognition with no apparent effects upon catalysis. A correlation between N7 pKa and Vmax suggests the deprotonation of N7 during the reaction, which must occur prior to subsequent glycosidic bond formation, appears to be partially rate-determining for the natural substrate. Comparison of the Kis of 7-methyl-substituted competitive inhibitors to the Kms of their corresponding substrates suggests that some substrates (including preQ1) are kinetically "sticky" (i.e., Km is equivalent to Kd) and other substrates have Kms that reflect catalytic rates as well as binding.

tRNA-guanine transglycosylase from Escherichia coli. Minimal tRNA structure and sequence requirements for recognition

Previously, we have demonstrated that the tRNA-guanine transglycosylase (TGT) from Escherichia coli is capable of utilizing an in vitro generated minihelix consisting of the anticodon stem and loop sequence of E. coli tRNA(Tyr) (Curnow, A. W., Kung, F. L., Koch, K. A., and Garcia, G. A. (1993) Biochemistry 32, 5239-5246). This suggests that the tRNA structural motifs necessary for recognition comprise a loop at the end of a short helix. To gain further insight into the structural requirements for TGT recognition, we have investigated the conformation of this minimal substrate. Thermal denaturation studies and kinetic analyses at 20 and 37 degrees C indicate that this minihelix is predominantly melted at 37 degrees C and that the melted conformation is not a substrate for TGT. This is confirmed by the determination that a non-helical analogue of the minihelix is not a substrate for TGT at either temperature. Two additional minihelices designed to be stable at 37 degrees C, ECYMH (a 4-base pair extension of the previous minihelix) and SCDMH (a yeast tRNA(Asp) analogue of ECYMH), were generated and characterized. Finally, several sequence mutants of SCDMH, focusing on the G30U40 base pair and U33G34U35 loop sequence, have been produced, and kinetic parameter determinations have been performed at 37 degrees C. Our results are consistent with a recent report (Nakanishi, S., Ueda, T., Hori, H., Yamazaki, N., Okada, N., and Watanabe, K. (1994) J. Biol. Chem. 269, 32221-32225) indicating that a UGU sequence in a 7-base loop is the minimal requirement for TGT recognition.

tRNA-guanine transglycosylase from Escherichia coli is a zinc metalloprotein. Site-directed mutagenesis studies to identify the zinc ligands

tRNA-guanine transglycosylase (TGT) from Escherichia coli catalyzes the exchange of the queuine precursor, preQ1, into tRNA as part of the biosynthetic pathway for the posttranscriptionally modified base, queuine. No significant sequence homologies exist between TGT and any of the proteins in the GenBank database. However, an unusual arrangement of cysteine residues was observed upon manual examination of the TGT sequence. Comparison of this sequence (residues 302-321) revealed similarities to structural zinc-binding motifs in proteins of known structure [Jaffe (1993) Comments Inorg. Chem. 15, 67-93]. Within this region of the TGT sequence, there are six residues (four cysteines and two histidines), any four of which could serve as the ligands to the zinc. We report here that wild-type TGT contains ca. 0.8 mol of zinc/mol of subunit, determined by atomic emission spectrometry. In order to determine which enzyme residues are serving as the ligands to the zinc, site-directed mutagenesis studies have been performed. Gross structural probes (native PAGE and CD spectra), enzyme activity assays, and tRNA-binding assays indicate that cysteines 302, 304, and 307 and histidine 317 are the ligands to the zinc. These results also suggest that the zinc site is necessary for TGT homotrimer formation and for tRNA binding.

Molecular mechanisms of the antihormonal and antiimplantation effects of norethisterone and its A-ring reduced metabolites

Norethisterone (NET) has been used as a contragestational postcoital agent. It is biotransformed to 5 alpha dihydro-NET (5 alpha-NET) and 3 beta,5 alpha tetrahydro-NET (3 beta,5 alpha-NET) in target tissues. The participation of these metabolites in NET effects is unknown. We have examined the antiimplantation and antiprogestational effects of NET and its metabolites, in adult mated female rabbits, by assessing the number of implantation sites and the expression products of the uteroglobin (UTG) gene in the uterus, and by comparing them with those of RU-486 and estradiol. Steroids were daily administered s.c. at several doses for 7 consecutive days, starting 24 hr after coitus. To assure that fertilization occurred in all animals, the presence of early pregnancy factor was determined. The results demonstrated that high doses (5 mg/kg) of NET reduced both implantation and the expression of the UTG gene. On the other hand, lower doses (1.5 mg/kg) of 5 alpha-NET produced an antiimplantation effect and suppressed UTG synthesis and its mRNA. These effects were similar to those of RU-486. At lower doses (1 mg/kg), both estradiol and the estrogenic metabolite 3 beta,5 alpha-NET were also effective in inhibiting implantation and UTG gene expression. The overall results suggest that NET metabolites exert antiimplantation and antiprogestational effects through their interaction with progesterone and estrogen receptors, and provide an explanation for the molecular mechanisms involved in the postcoital contraceptive action of NET.

Norethisterone metabolites modulate the uteroglobin and progesterone receptor gene expression in prepubertal rabbits

Norethisterone (NET) is a synthetic progestin, used as a contraceptive agent, that is biotransformed at target tissues into 5 alpha-NET and 3 beta,5 alpha-NET, which possess different pharmacological properties. The effects of these metabolites on the expression of uteroglobin (UG) and progesterone receptor (PR) genes, both regulated by progesterone (P4), were evaluated in the uterus of prepubertal female rabbits that were simultaneously treated with P4 (1.0 mg) for 5 consecutive days. As determined by Western and Northern blot analyses, 5 alpha-NET inhibited the P4-induced UG gene expression in a dose-dependent manner. A similar inhibition was observed with the administration of RU-486. The estrogenic agent 3 beta,5 alpha-NET and estradiol at a dose of 1.0 mg also inhibited the UG gene expression induced by P4. Both 5 alpha-NET and 3 beta,5 alpha-NET blocked the PR down-regulation induced by P4 as assessed by Western and Northern blot methods. The inhibition of UG synthesis and PR down-regulation by 5 alpha-NET and 3 beta,5 alpha-NET indicates that these NET metabolites possess antiprogestational properties.

A prospective evaluation of thoracoscopy for the diagnosis of penetrating thoracoabdominal trauma

Penetrating thoracoabdominal trauma presents a difficult diagnostic dilemma. Violation of the diaphragm may be very difficult to establish. Conventional diagnostic procedures such as chest radiography, computed tomography, and diagnostic peritoneal lavage have been shown to be unreliable. Mandatory exploratory celiotomy carries a 20%-30% negative rate. Twenty-eight patients with penetrating thoracoabdominal trauma over a 6-month period were prospectively evaluated by thoracoscopy at a major urban trauma center. All patients were hemodynamically stable, had no indications for immediate celiotomy, and demonstrated thoracic injury on chest radiography or physical examination. All thoracoscopy was performed in the operating room under general anesthesia. Patients consisted of 25 males and 3 females with an age range of 15-48 years. Mechanism of injury consisted of 24 stab wounds and 4 gunshot wounds. Twelve of the procedures were for right chest wounds and 16 involved the left hemithorax. Diaphragmatic injury was identified at thoracoscopy in 9 patients (32%), with all confirmed and repaired at celiotomy. Eight of 9 patients (89%) undergoing celiotomy were found to have significant intra-abdominal injuries requiring surgical repair. Thoracoscopy was also useful for evacuation of blood from the pleural space. There were no procedure-related complications. Thoracoscopy is a safe, accurate, reliable diagnostic technique for evaluating thoracoabdominal penetrating trauma. It is less invasive than celiotomy and has the added benefit of diagnosis and therapy of the intrathoracic injuries.

An oligonucleotide-directed, in vitro mutagenesis method using ssDNA and preferential DNA amplification of the mutated strand

The sequential addition of primers in a PCR enables one to preferentially amplify one of the two strands of a heteroduplex DNA template. This serves as the basis for a novel site-directed mutagenesis technique involving a heteroduplex DNA template that has been generated from a single-stranded, wild-type template and one or more mutagenic oligonucleotides. This preferential PCR method yields a mutation efficiency greater than 90% (consistent with the theoretical estimate for the method). The ability to generate multiple mutants also enables the screening of potential mutants by restriction endonuclease digestion.

A versatile and general prokaryotic expression vector, pLACT7

We have previously reported the constitutive over-expression of the tRNA-guanine transglycosylase (TGT) from plasmid pTGT1 in Escherichia coli. To obtain a controllable expression system for TGT, we have subsequently cloned the tgt gene into pET21b. Though the overexpression of TGT is inducible in pET21b, the plasmid has a low copy number, a poor yield of single-stranded DNA and relies on an E. coli strain that produces T7 RNA polymerase for protein expression. We have combined the features of pTZ18U and pET21b and have constructed a versatile plasmid pLACT7 that has a high copy number, a high yield of single-stranded DNA and both the T7 and lac promoters for protein expression in a wide variety of E. coli strains.

Serine 90 is required for enzymic activity by tRNA-guanine transglycosylase from Escherichia coli

An Escherichia coli mutant described by Noguchi et al. [Noguchi, S., et al. (1982) J. Biol. Chem. 275, 6544-6550] contains tRNA lacking the hypermodified wobble nucleoside queuosine (Q) due to an inactive tRNA-guanine transglycosylase (TGT). TGT catalyzes the posttranscriptional base exchange of the Q precursor preQ1 with the genetically encoded guanine in tRNA(Asp,Asn,His,Tyr). The mutant tgt gene was cloned and sequenced; it contained a single point mutation resulting in the change of serine 90 to phenylalanine. Overexpression of the mutant gene yielded TGT(S90F) that showed a reduced solubility and did not purify in the same fashion as the wild-type enzyme. TGT(S90F) has no detectable enzymic activity. To determine whether serine 90 performs a catalytic role in the TGT reaction or whether the loss of activity was caused solely by a conformational change of the enzyme, we used site-specific mutagenesis to construct serine-to-alanine (S90A) and serine-to-cysteine (S90C) mutants. Both S90A and S90C mutants were purified in a manner identical to that used for the wild-type enzyme. SDS-PAGE of dimethyl suberimidate-cross-linked mutants showed a pattern identical to that of the wild-type TGT, indicative of a trimeric quaternary structure. Native PAGE of wild-type and mutant TGTs in the absence and presence of substrate tRNA exhibited band shifts indicating that both mutants retain the ability to bind tRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

tRNA-guanine transglycosylase from Escherichia coli: recognition of dimeric, unmodified tRNA(Tyr)

In order to probe the interaction between tRNA and the tRNA hypermodifying enzyme, tRNA-guanine transglycosylase (TGT) from Escherichia coli, we have undertaken the generation of E coli tRNA(Tyr) and analogues. During efforts to adapt currently available in vitro transcription techniques we encountered difficulties attributable to dimerization of the tRNA products. E coli tRNA(Tyr) has previously been characterized for its ability to form a dimer in solutions of suitable salt concentrations at appropriate temperatures (Yang SK, Söll DG, Crothers DM (1972) Biochemistry 11, 2311-2320; Rordorff BF, Kearns DR (1976) Biochemistry 15, 3320-3330). We have applied similar techniques to our unmodified analogue of E coli tRNA(Tyr) and produced both monomeric and dimeric forms of E coli tRNA(Tyr). In this report we find that the dimer does serve as a substrate for modification by TGT. While both the conformers are equal in terms of Vmax (within experimental error) a 2.5-fold increase in KM occurs when going from monomer to dimer. This suggests that TGT preferentially binds the monomer but once either conformer is bound will catalyze the modification reaction equally well. We have also compared the results for the two conformers to our previous data of an RNA minihelix corresponding to the anticodon arm of E coli tRNA(Tyr). Here we find that our earlier conclusion, that the recognition elements for TGT are localized within the anticodon arm of cognate tRNAs, is supported.

Reaction of modified and unmodified tRNA(Tyr) substrates with tyrosyl-tRNA synthetase (Bacillus stearothermophilus)

Three species of tRNA(Tyr) have been examined as substrates for the transfer reaction of the tyrosyl-tRNA synthetase (TyrRS) from Bacillus stearothermophilus: Escherichia coli tRNA(Tyr), B. stearothermophilus tRNA(Tyr) expressed in E. coli, and B. stearothermophilus tRNA(Tyr) that has been transcribed in vitro. The binding of the first two substrates to TyrRS may be readily monitored by stopped-flow studies of tryptophan fluorescence to give the rate and equilibrium constants. The in vitro-transcribed tRNA(Tyr), which lacks the modified bases queuosine and 2-(methylthio)-N6-isopentenyladenosine in the anticodon loop, does not cause a significant change in tryptophan fluorescence upon binding. The three tRNA(Tyr) substrates exhibit very similar steady-state kinetics in the charging reaction. Pre-steady-state kinetics of the transfer reaction, monitored by stopped-flow measurements of the change in protein fluorescence on the addition of tRNA(Tyr) to the E.Tyr-AMP complex, show two exponential changes for the modified tRNA(Tyr) substrates. The first is that due to substrate binding. The second has an identical rate to the single change observed for the reaction with the in vitro-transcribed tRNA(Tyr) and to that monitored by quenched-flow measurements on the formation of Tyr-tRNA(Tyr). Hence, the transfer reaction can be observed by stopped-flow. The dissociation constants (KtRNA) of tRNA from the enzyme and rates of tyrosine transfer (k4) show that all three tRNA molecules are kinetically equivalent substrates for TyrRS. The value of k4 is also similar to that found for authentic tRNA(Tyr) from B. stearothermophilus.(ABSTRACT TRUNCATED AT 250 WORDS)

tRNA-guanine transglycosylase from Escherichia coli. Overexpression, purification and quaternary structure

tRNA-guanine transglycosylase (TGT) is the enzyme responsible for the posttranscriptional modification of specific tRNAs (Asn, Asp, His and Tyr) with queuine. In E. coli this modification occurs via a two-step reaction: (1) TGT-catalyzed base exchange of guanosine-34 with preQ1 (7-aminomethyl-7-deazaguanine) and (2) addition of a cyclopentenediol moiety to the preQ1-34 tRNA. E. coli TGT is normally expressed at very low levels (approximately 1 mg from 500 g cells). The sequence of the queuine operon of E. coli has recently been reported by Reuter et al. (1991). We have cloned the tgt gene into an overexpressing vector in order to provide a more efficient preparation of TGT. A simple, four-step purification scheme yields 78 mg of homogeneous TGT per liter of cell culture (A600 = 5 to 6). Amino-terminal protein sequencing confirms the identity of the recombinant protein and indicates that the initiator methionine is retained in the mature form. Native-PAGE of TGT and SDS-PAGE of cross-linked TGT are most consistent with a hexameric quaternary structure for the enzyme. The cross-linking data also suggests that the enzyme exists as a dimer of trimers of identical 42.5 kDa subunits (total M(r) = 255 kDa. The enzyme is inactivated by cross-linking with the bisimidoester, dimethylsuberimidate. Substrate (tRNA) protects the enzyme against cross-linking and inactivation by dimethylsuberimidate and against inactivation by modification with ethylacetimidate, a monofunctional, imidoester. This indicates that the enzymic residues (presumably lysines) that are involved in cross-linking and the inactivation are in the active site of the enzyme.

tRNA-guanine transglycosylase from Escherichia coli: gross tRNA structural requirements for recognition

tRNA-guanine transglycosylase (TGT) is the enzyme responsible for the post-transcriptional modification of specific tRNAs (those for Asn, Asp, His, and Tyr) with the hypermodified base, queuine. In Escherichia coli this enzyme catalyzes the exchange of guanine-34 in the anticodon with preQ1, which is subsequently further modified to queuine. There is evidence that such hypermodified tRNA molecules may play a role in the control of cell proliferation and differentiation. In order to perform detailed, in vitro mechanistic studies and to probe the tRNA-enzyme interaction, we have generated unmodified E. coli tRNA(Tyr) and truncated analogues using an in vitro RNA synthesis system suggested by Milligan and Uhlenbeck [Milligan, J. F., & Uhlenbeck, O. C. (1989) Methods Enzymol. 180, 51-62]. From this system we have generated three tRNA analogues totally devoid of any post-transcriptional modifications. In order to compare the unmodified tRNA with the true physiological substrate for TGT, that is, tRNA that contains all modified bases except queuine, we have isolated E. coli tRNA(Tyr) from an overexpressing clone in a TGT-deficient strain of E. coli. We report here that unmodified, full-length tRNA(Tyr) serves as a substrate for TGT with kinetic parameters that are, within experimental error, the same as those for in vivo isolated tRNA(Tyr). This indicates that other post-transcriptional modifications have negligible effects upon TGT recognition of tRNA. A 17-base oligoribonucleotide, corresponding to the anticodon loop and stem, is also a substrate for TGT with only a 20-fold loss in Vmax/KM, versus the full-length tRNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Metal ion dependence of phosphorothioate ATP analogues in the Bacillus stearothermophilus tyrosyl-tRNA synthetase reaction

Pre-steady-state kinetic analyses on the formation of tyrosyl adenylate from tyrosine and each of the four diastereomers of alpha- and beta-phosphorothioate adenosine triphosphates [ATP alpha S and ATP beta S; Eckstein, F., & Goody, R. (1976) Biochemistry 15, 1685-1691; Yee, D., Armstrong, V. W., & Eckstein, F. (1979) Biochemistry 18, 4116-4123] were performed in the presence of Mg2+, Co2+, and Cd2+ as the divalent metal ion cofactor. A modest preference of 5.5-fold in kappa 3/KA' (where kappa 3 is the rate constant for tyrosyl adenylate formation and KA' is the dissociation constant for ATP, or phosphorothioate ATP, from the E.Tyr.metal.ATP complex) for the Sp ATP alpha S diastereomer and the absence of an inversion of preference when the metal ion is changed suggest that there is a stereospecific enzyme-alpha-phosphate interaction and that there is no direct metal ion interaction with the alpha-phosphate. The extent of reaction of the ATP alpha S diastereomers (30-50%) implies that these analogues are more susceptible to the hydrolytic site reaction previously reported for this enzyme [Wells, T. N. C., & Fersht, A. R. (1986) Biochemistry 25, 1881-1886]. The strong preference in kappa 3/KA' for the RP ATP beta S diastereomer (16-fold for Mg2+ and 50-fold for Co2+) is indicative of a stereospecific interaction with the pro SP beta oxygen of ATP.(ABSTRACT TRUNCATED AT 250 WORDS)