Structural basis of translational control by Escherichia coli threonyl tRNA synthetase

Escherichia coli threonyl-tRNA synthetase (ThrRS) represses the translation of its own messenger RNA by binding to an operator located upstream of the initiation codon. The crystal structure of the complex between the core of ThrRS and the essential domain of the operator shows that the mRNA uses the recognition mode of the tRNA anticodon loop to initiate binding. The final positioning of the operator, upon which the control mechanism is based, relies on a characteristic RNA motif adapted to the enzyme surface. The finding of other thrS operators that have this conserved motif leads to a generalization of this regulatory mechanism to a subset of Gram-negative bacteria.

The role of the basic surgical skills course in the acquisition and retention of laparoscopic skill

BACKGROUND

This study assesses the transfer of laparoscopic skills to a group of Basic Surgical Trainees (BST) attending the Basic Surgical Skills (BSS) course.

METHODS

The virtual reality simulator MIST-VR was used to assess 13 trainees before and after the course and again 3 weeks and 3 months later. Analysis of kinematic data using the Imperial College Surgical Assessment Device gave measures of distance traveled, distance efficiency ratio, time taken, number of errors made, and number of movements made in completing a virtual laparoscopic task. The performance of the group was compared to a control group who underwent no training.

RESULTS

All parameters improved significantly after the course, with the exception of distance traveled by the instruments. All outcome measures were significantly improved at 3 weeks. The control group showed a nonsignificant trend toward improvement in all parameters.

CONCLUSIONS

The Basic Surgical Skills course produces quantifiable improvements in laparoscopic skill that are measurable by MIST-VR. There is a learning effect associated with using MIST-VR alone.

Documentation and log keeping: ensuring your work does what you intend it to do

Maintaining regular documentation, such as a log-book, can be an organization's most important asset when dealing with radiation protection issues, both normal and abnormal. When an organization is faced with litigation, proper documentation of events can ensure that a record is acceptable and, by extension, that the data itself is acceptable. A record of events will not preclude litigation, nor will it guarantee that an organization will prevail in a court of law, but it will provide evidence and credibility that could favorably affect the outcome of litigation. An organization can ensure that the documents it creates and maintains are as effective as possible by being aware of the legal consequences of documenting events and taking appropriate steps to conform to standards for admission of documentation. Misconceptions about log keeping such as recording only events that are likely to result in litigation, rather than recording all events, can prevent a record from being admissible as evidence. Because of the amount of effort and time put into documentation, and the reliance placed on its contents, it is important for an organization to ensure that a record will do what it is intended to do, namely to accurately record activities. Issues discussed in this article include the legal basis of documentary evidence, what and what not to record, when and how to record it, and how to strengthen the records kept.

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.

Aspartyl tRNA-synthetase from Escherichia coli: flexibility and adaptability to the substrates

The crystal structure of aspartyl-tRNA synthetase from Escherichia coli has been determined to a resolution of 2.7 A. The structure is compared to the same enzyme co-crystallized with tRNA(Asp) and containing aspartyl adenylate or ATP. The asymmetric unit contains three monomers of the enzyme. While most parts of the protein show no significant differences in the three monomers, a few regions cannot be superimposed. Those regions are characterized by a high B-factor, and consist mostly of loops that make contacts with the tRNA in the complexes. The flexibility of the protein is seen at a global level, by the observation of a 10 to 15 degrees rotation of the N-terminal and insertion domains upon tRNA binding, and at the level of the individual amino acid residues, by main-chain and side-chain rearrangements. In contrast to these induced-fit conformational changes, a few residues essential for the tRNA anticodon or aspartyl-adenylate recognition exist in a predefined conformation, ensured by specific interactions within the protein.

Zinc ion mediated amino acid discrimination by threonyl-tRNA synthetase

Accurate translation of the genetic code depends on the ability of aminoacyl-tRNA synthetases to distinguish between similar amino acids. In order to investigate the basis of amino acid recognition and to understand the role played by the zinc ion present in the active site of threonyl-tRNA synthetase, we have determined the crystal structures of complexes of an active truncated form of the enzyme with a threonyl adenylate analog or threonine. The zinc ion is directly involved in threonine recognition, forming a pentacoordinate intermediate with both the amino group and the side chain hydroxyl. Amino acid activation experiments reveal that the enzyme shows no activation of isosteric valine, and activates serine at a rate 1,000-fold less than that of cognate threonine. This study demonstrates that the zinc ion is neither strictly catalytic nor structural and suggests how the zinc ion ensures that only amino acids that possess a hydroxyl group attached to the beta-position are activated.

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.

Transmembrane signaling across the ligand-gated FhuA receptor: crystal structures of free and ferrichrome-bound states reveal allosteric changes

FhuA protein facilitates ligand-gated transport of ferrichrome-bound iron across Escherichia coli outer membranes. X-ray analysis at 2.7 A resolution reveals two distinct conformations in the presence and absence of ferrichrome. The monomeric protein consists of a hollow, 22-stranded, antiparallel beta barrel (residues 160-714), which is obstructed by a plug (residues 19-159). The binding site of ferrichrome, an aromatic pocket near the cell surface, undergoes minor changes upon association with the ligand. These are propagated and amplified across the plug, eventually resulting in substantially different protein conformations at the periplasmic face. Our findings reveal the mechanism of signal transmission and suggest how the energy-transducing TonB complex senses ligand binding.

Quality of life in cardiac patient research: a meta-analysis

This article reports a meta-analysis of 84 studies of quality of life (QOL) in cardiac patient populations published in the 5-year period 1987-1991. Selected methodologies and substantive characteristics of the studies are described. An overall effect size of .31 indicated a small but significant positive effect of pharmacologic, mechanical, surgical, nursing, or other treatment on QOL. No negative effect of treatment was found for any cardiovascular diagnostic category. Homogeneity analysis revealed eight potential moderators of the overall effect size: quality of study, gender of sample, time dimension, sampling method, intervention, marital status of subjects, quality-of-life dimension measured, and sample size.

32P and beta emitting radionuclides in microbiology and cell biology

Microbiology and cell biology researchers make extensive use of beta emitting nuclides. Because of the short half-lives or difficulty of direct measurement some researchers do not view radionuclide use with proper care and respect. Radionuclide use in microbiology and cell biology research is unique. Review of the isotopes and processes may be useful to the health physicist and research alike.

Conformational flexibility of tRNA: structural changes in yeast tRNA(Asp) upon binding to aspartyl-tRNA synthetase

The availability of several X-ray structures at atomic resolution of tRNA(Asp) from yeast, both in its free state and complexed with its cognate tRNA-synthetase, enables a detailed examination of the conformational changes due to interaction with the enzyme. Although the molecule conserves its general L shape, its conformation undergoes important modifications. They may be described as a bending of the two arms which brings the 3' acceptor end and the anticodon part closer together, completed by a drastic change of the anticodon loop, which puts the anticodon bases in a more exposed position, facilitating their interaction with the synthetase. The packing interactions in the crystals are also discussed. Finally, the results of protection studies by chemical probes in solution are discussed in view of the RNA-protein contacts observed in the crystals.

Crystal structure of histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate

The crystal structure at 2.6 A of the histidyl-tRNA synthetase from Escherichia coli complexed with histidyl-adenylate has been determined. The enzyme is a homodimer with a molecular weight of 94 kDa and belongs to the class II of aminoacyl-tRNA synthetases (aaRS). The asymmetric unit is composed of two homodimers. Each monomer consists of two domains. The N-terminal catalytic core domain contains a six-stranded antiparallel beta-sheet sitting on two alpha-helices, which can be superposed with the catalytic domains of yeast AspRS, and GlyRS and SerRS from Thermus thermophilus with a root-mean-square difference on the C alpha atoms of 1.7-1.9 A. The active sites of all four monomers are occupied by histidyl-adenylate, which apparently forms during crystallization. The 100 residue C-terminal alpha/beta domain resembles half of a beta-barrel, and provides an independent domain oriented to contact the anticodon stem and part of the anticodon loop of tRNA(His). The modular domain organization of histidyl-tRNA synthetase reiterates a repeated theme in aaRS, and its structure should provide insight into the ability of certain aaRS to aminoacylate minihelices and other non-tRNA molecules.

The class II aminoacyl-tRNA synthetases and their active site: evolutionary conservation of an ATP binding site

Previous sequence analyses have suggested the existence of two distinct classes of aminoacyl-tRNA synthetase. The partition was established on the basis of exclusive sets of sequence motifs (Eriani et al. [1990] Nature 347:203-306). X-ray studies have now well defined the structural basis of the two classes: the class I enzymes share with dehydrogenases and kinases the classic nucleotide binding fold called the Rossmann fold, whereas the class II enzymes possess a different fold, not found elsewhere, built around a six-stranded antiparallel beta-sheet. The two classes of synthetases catalyze the same global reaction that is the attachment of an amino acid to the tRNA, but differ as to where on the terminal adenosine of the tRNA the amino acid is placed: class I enzymes act on the 2' hydroxyl whereas the class II enzymes prefer the 3' hydroxyl group. The three-dimensional structure of aspartyl-tRNA synthetase from yeast, a typical class II enzyme, is described here, in relation to its function. The crucial role of the sequence motifs in substrate binding and enzyme structure is high-lighted. Overall these results underline the existence of an intimate evolutionary link between the aminoacyl-tRNA synthetases, despite their actual structural diversity.

Angiotensin and bradykinin peptides in the TGR(mRen-2)27 rat

The transgenic TGR(mRen-2)27 rat, in which the Ren-2 mouse renin gene is transfected into the genome of the Sprague-Dawley rat, develops severe hypertension at a young age that responds to inhibitors of angiotensin-converting enzyme and to antagonists of the type 1 angiotensin II (Ang II) receptor. Despite this evidence that the hypertension is Ang II dependent, TGR(mRen-2)27 rats have suppressed renal renin and renin mRNA content, and there is controversy concerning the plasma levels of renin and Ang II in these rats. We investigated the effect of the transgene on circulating and tissue levels of angiotensin and bradykinin peptides in 6-week-old male homozygous TGR(mRen-2)27 rats. Systolic blood pressure of TGR(mRen-2)27 rats was 212 +/- 4 mm Hg (mean +/- SEM, n = 25) compared with 108 +/- 2 mm Hg (n = 29) for age- and sex-matched Sprague-Dawley rats. Compared with control rats, TGR(mRen-2)27 rats had increased plasma levels of active renin (4.5-fold), prorenin (300-fold), and Ang II (fourfold) as well as tissue levels of Ang II (twofold to fourfold in kidney, adrenal, heart, aorta, brown adipose tissue, and lung and 18-fold in brain). Plasma angiotensinogen levels were reduced to 73% of control, and plasma aldosterone levels were increased fourfold. Plasma angiotensin-converting enzyme was reduced to 64% of control. Compared with control rats, TGR(mRen-2)27 rats had increased bradykinin levels in brown adipose tissue (1.9-fold) and lung (1.6-fold).(ABSTRACT TRUNCATED AT 250 WORDS)

Electrostatic potential in aminoacylation by aspartyl-tRNAs synthetase

Based upon the X-ray structures of complexes between tRNAAsp and aspRS including ATP or Asp-AMP, several electrostatic potentials were calculated by solving the Poisson-Boltzmann equation. The potentials indicate clearly that a Mg2+ ion is essential for binding of ATP and that aspartate is identified electrostatically. The alpha-carboxyl group is forced to contact with the alpha-phosphorus atom of ATP, suggesting its inversion to form an Asp-AMP. When the cognate tRNA is bound to the aspRS:Asp-AMP complex, the 3'-hydroxyl group is located in an electrostatically favorable position to transfer the amino acid as a class II aminoacylation.

X-ray structure at 1.55 A of toxin gamma, a cardiotoxin from Naja nigricollis venom. Crystal packing reveals a model for insertion into membranes

The crystal structure of toxin gamma from Naja nigricollis has been solved and refined to 1.55 A resolution. The final R-factor, computed with all X-ray data available, is 17.9%. The three-dimensional structure is characterized by a core formed by two beta-sheets organized in three extended loops. It is similar to that of cardiotoxin V4II from Naja mossambica mossambica, with the exception of the hydrophobic loop I. The flexibility and variability of the loops contrast sharply with the rigidity of the molecular core and its high degree of structural conservation among the cardiotoxin family. The most flexible loop II adopts different conformations in the three monomers forming the crystal asymmetric unit. These monomers form a trimer around an approximate 3-fold axis, with conserved hydrophobic side-chains on the outside and hydrophilic residues in the central channel or involved in interactions with the other molecules. The trimer thus resembles a membrane protein with a central channel that could allow the passage of small ions. It is proposed as a model for the insertion of cardiotoxin into a membrane.

The active site of yeast aspartyl-tRNA synthetase: structural and functional aspects of the aminoacylation reaction

The crystal structures of the various complexes formed by yeast aspartyl-tRNA synthetase (AspRS) and its substrates provide snapshots of the active site corresponding to different steps of the aminoacylation reaction. Native crystals of the binary complex tRNA-AspRS were soaked in solutions containing the two other substrates, ATP (or its analog AMPPcP) and aspartic acid. When all substrates are present in the crystal, this leads to the formation of the aspartyl-adenylate and/or the aspartyl-tRNA. A class II-specific pathway for the aminoacylation reaction is proposed which explains the known functional differences between the two classes while preserving a common framework. Extended signature sequences characteristic of class II aaRS (motifs 2 and 3) constitute the basic functional unit. The ATP molecule adopts a bent conformation, stabilized by the invariant Arg531 of motif 3 and a magnesium ion coordinated to the pyrophosphate group and to two class-invariant acidic residues. The aspartic acid substrate is positioned by a class II invariant acidic residue, Asp342, interacting with the amino group and by amino acids conserved in the aspartyl synthetase family. The amino acids in contact with the substrates have been probed by site-directed mutagenesis for their functional implication.