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PubMed2000

Kinetic proofreading scanning models for eukaryotic translational initiation: the cap and poly(A) tail dependency of translation.

Two simplified kinetic proofreading scanning (KPS) models were proposed to describe the 5' cap and 3' poly(A) tail dependency of eukaryotic translation initiation. In Model I, the initiation factor complex starts scanning and unwinding the secondary structure of the 5' untranslated region (UTR) from the 5' terminus of mRNA. In Model II, the initiation factor complex starts scanning from any binding site in the 5' UTR. In both models, following ATP hydrolysis, the initiation factor complex either dissociates from mRNA or continues to scan and unwind RNA secondary structure in the 5' UTR. This step repeats n times until the AUG codon is reached. These two models show very different cap and/or poly(A) tail dependency of translation initiation. The models predict that both cap and poly(A) tail dependencies of translation, and translatability of mRNAs are coupled with the structure of 5' UTR: the translation of mRNA with structured 5' UTR is strongly cap- and poly(A) tail-dependent; while translation of mRNA with unstructured 5' UTR is less cap- and poly(A) tail-dependent. We use these two models to explain: (1) the cap and poly(A) tail dependence of translation; (2) the effect of exogenous poly(A) on translation; (3) repression of host mRNA and translation of late adenovirus mRNA in the late phase of adenovirus infection; (4) repression of host mRNA and translation of Vaccinia virus mRNA in virus-infected cell; (5) heat shock repression of translation of normal mRNA and stimulation of translation of hsp mRNA; and (6) the synergistic effect of cap and poly(A) tail on stimulating translation. The kinetic proofreading scanning models provide a coherent interpretation of those phenomena.

5' Untranslated Regions↗
PubMed1993

The short tail-fiber of bacteriophage T4: molecular structure and a mechanism for its conformational transition.

Electron microscopy, image processing and computational sequence analysis were used to investigate the structure of the short tail-fiber of bacteriophage T4. This molecule, an oligomer of gp12, is an adhesin that binds the virion irreversibly to the bacterial surface. Short tail-fibers were isolated from mutant-infected cells in which gp12 is synthesized and assembled correctly, but not incorporated into virions. Visualized in negative stain, these filamentous molecules are approximately 38 nm in total length, with an arrowhead-shaped head (approximately 10 nm long by 6 nm wide), a 24-nm shaft of uniform width (approximately 3.8 nm), and a small, seemingly flexible, tail. The primary sequence contains a domain consisting of tandem quasi-repeats, each about 40 residues long, extending from approximately residue 50 to residue 320. Molecular mass analyses by scanning transmission electron microscopy confirm that the molecule is a trimer. The masses of the head, shaft, and tail domains are consistent with (trimers of) the carboxy-terminus, the repeat region, and the amino-terminus, respectively. When short tail-fibers are visualized extending from baseplates, their heads are distal, i.e., detached, implying that it is the tail that remains in contact with the baseplate. Analysis of the molecules' curvature properties detects three hinge-sites: these suggest how the short tail-fiber may be initially accommodated in a compact conformation in the "hexagon" state of the baseplate, from which it converts to the extended conformation when the baseplate switches into its "star" state.

Amino Acid Sequence↗
PubMed1987

Intrathecal dynorphin(1-13) results in an irreversible loss of the tail-flick reflex in rats.

Intrathecal injection of dynorphin produced a loss of the tail-flick reflex that lasted throughout the 14-day experimental period whereas, the inclined plane test of motor function and tail-shock vocalization recovered within an hour. An important aspect of the loss of the tail-flick reflex was that it was an all-or-none event. At any dose of tail-flick latency either remained unchanged when compared with pre-injection latencies or the latency was elevated to the cut off time of 14 s. The ED50's +/- S.E.M. for tail-flick, inclined plane and tail-shock vocalization were 65.4 +/- 5.0, 67.7 +/- 5.0 and 68.0 +/- 3.9 nmol respectively. Results from the hot-plate test revealed no statistical difference between saline and dynorphin injected animals one day following the injection. Animals injected with morphine sulphate s.c. lost the tail-flick reflex but completely recovered by 24 h. Histology of the spinal cord of animals treated with dynorphin 24 h prior to sacrifice revealed dead neurons primarily in the ventral horn with little or no damage in the dorsal horn. These data demonstrate that dynorphin(1-13) injected intrathecally results in a rather specific neurotoxic action in the spinal cord.

Animals↗
PubMed1992

Kappa opiate receptors mediate tail-shock induced antinociception at spinal levels.

Previous work has demonstrated that 3 pharmacologically and neuroanatomically distinct analgesia systems can be sequentially activated by increasing numbers of transcutaneous tail-shock. To date, the categorization of the early (after 2 tail-shocks) and late (after 80-100 tail-shocks) analgesias as opiate-mediated has been based on the ability of systemic naltrexone and morphine tolerance to block these effects. In contrast, the analgesia observed after 5-40 tail-shocks is unaffected by these manipulations, leading to its categorization as non-opiate. The present work and the following companion paper were aimed at identifying the neuroanatomical loci at which endogenous opiates exert their analgesic effects in this tail-shock paradigm and, further, to identify which opiate receptor subtypes are involved. The 3 experiments included in the present paper focus on the role of spinal opiates in tail-shock induced analgesia. The first experiment demonstrates that the tail-shock parameters used do not directly activate pain suppressive circuitry within the spinal cord, but rather activate centrifugal pain modulation circuitry originating within the brain. The last two experiments examine the effect of intrathecal microinjection of either naltrexone (a relatively non-selective opiate receptor antagonist), binaltorphimine (kappa receptor antagonist), Cys2-Tyr3-Orn5-Pen7-amide (CTOP) (mu receptor antagonist), or naltrindole (delta receptor antagonist). Taken together, these latter 2 experiments demonstrate that both the early (after 2 shocks) and late (after 80-100 shocks) opiate analgesias are mediated by kappa opiate receptors within the spinal cord.

Analysis of Variance↗
PubMed1993

Enhanced recovery and purification of Aspergillus glucoamylase from Saccharomyces cerevisiae by the addition of poly(aspartic acid) tails.

Poly(aspartic acid) tails of different lengths were fused to the glucoamylase (GA) of Aspergillus awamori by genetic engineering techniques. Tails consisting of 5, 7, and 10 aspartate residues were fused to the N-terminus of the full-length mature GA (aa 1-616) downstream from the intact leader peptide to produce fusion proteins designated GAND5, GAND7, and GAND10, respectively. Three fusion proteins with C-terminal tails were also constructed, designated GACD0, GACD5, and GACD10 (0, 5, and 10 aspartate residues, respectively). For the C-terminal fusion proteins, the tails were fused to a catalytically active but truncated form of GA (aa 1-484). All of the charged tails had the general sequence Met-Ala-Aspn-Tyr, where n = 0, 5, 7, or 10. The modified genes were expressed in the yeast Saccharomyces cerevisiae and the proteins secreted into the culture medium. The enzymes were subsequently purified by affinity chromatography. The specific activity of each purified enzyme was found to be comparable to the wild-type enzyme. The C-terminal tails did not interfere with expression, whereas decreased extracellular glucoamylase activities corresponding to increased tail length were found for the N-terminal fusion proteins. Amino-terminal amino acid sequence analysis of the purified GAND proteins confirmed the authenticity of the amino termini of the modified proteins and showed that both the leader peptidase and KEX2 protease cleavages had occurred faithfully. The increased net negative charge of the GAND and GACD proteins was indicated by both nondenaturing PAGE and isoelectric focusing.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗
PubMed1988

Apparent hyperalgesia after lesions of the descending serotonergic pathways is due to increased tail skin temperature.

It has been suggested that the descending serotonergic pathways exercise a tonic inhibition on nociception in the spinal cord. In this study 5,6-dihydroxytryptamine (5,6-DHT, 20 micrograms base) injected intrathecally in rats reduced spinal serotonin concentration to 3.5% of control levels without significantly affecting spinal noradrenaline. The lesion reduced the mean tail-flick latency by approximately 35% and increased the mean tail skin temperature by approximately 3.5 degrees C; both parameters gradually returned to normal values within 2-3 weeks. Both in controls and in lesioned animals there was a highly significant negative correlation between tail skin temperature and tail-flick latency. Multiple regression analysis showed that the effect of lesioning on tail-flick latency was non-significant when the effect of skin temperature was taken into account. Thus the reduced tail-flick latency after lesions of descending serotonergic pathways, usually interpreted as increased nociception, may be due to changes in tail skin temperature.

5,6-Dihydroxytryptamine↗
PubMed1990

Two ubiquitin-long-tail fusion genes arranged as closely spaced direct repeats in barley.

Ubiquitin (Ubi) genes encode two types of fusion proteins: polyUbi with a varying number of direct repeats of Ubi, and Ubi-tail fusions with long or short basic C-terminal extensions. A barley (Hordeum vulgare) genomic clone has been isolated with two very similar, intronless genes encoding monoUbi-long-tail fusion peptides. The genes are arranged as direct repeats separated by 3 kb of DNA and account for two of the probable three long-tail genes in the haploid barley genome. Both genes are active and give rise to messengers about 800 nt long. The sequence of the encoded Ubi moieties is identical to the sequence of Ubi repeats of polyUbi precursors from barley and other plants. The basic tails of the peptides are 79 aa long and 71-72% homologous to corresponding sequences from yeast and man. Recently, it was found that the long and short tails are ribosomal proteins in yeast [Finley et al., Nature 338 (1989) 394-401] and the evolutionary conservation of the structure of the Ubi-tail fusion genes suggests that they serve the same function in plants. The similarity between yeast and barley Ubi-long-tail fusion genes may extend to the regulatory regions, since upstream activating sites characteristic of ribosomal protein-encoding genes in yeast (UASrpg) were found in the barley genes.

Amino Acid Sequence↗
PubMedDate not supplied

Fusion tails for the recovery and purification of recombinant proteins.

Several fusion tail systems have been developed to promote efficient recovery and purification of recombinant proteins from crude cell extracts or culture media. In these systems, a target protein is genetically engineered to contain a C- or N-terminal polypeptide tail, which provides the biochemical basis for specificity in recovery and purification. Tails with a variety of characteristics have been used: (1) entire enzymes with affinity for immobilized substrates or inhibitors; (2) peptide-binding proteins with affinity to immunoglobulin G or albumin; (3) carbohydrate-binding proteins or domains; (4) a biotin-binding domain for in vivo biotination promoting affinity of the fusion protein to avidin or streptavidin; (5) antigenic epitopes with affinity to immobilized monoclonal antibodies; (6) charged amino acids for use in charge-based recovery methods; (7) poly(His) residues for recovery by immobilized metal affinity chromatography; and (8) other poly(amino acid)s, with binding specificities based on properties of the amino acid side chain. Fusion tails are useful at the lab scale and have potential for enhancing recovery using economical recovery methods that are easily scaled up for industrial downstream processing. Fusion tails can be used to promote secretion of target proteins and can also provide useful assay tags based on enzymatic activity or antibody binding. Many fusion tails do not interfere with the biological activity of the target protein and in some cases have been shown to stabilize it. Nevertheless, for the purification of authentic proteins a site for specific cleavage is often included, allowing removal of the tail after recovery.

Amino Acids↗
PubMed2004

pH dependence of tailing in reversed-phase chromatography of a cationic dye: measurement of the strong adsorption site surface density.

A question that has interested Dr. J.J. Kirkland is addressed: what is the nature of the silanols that cause tailing to persist at low pH in reversed-phase chromatography? Chromatograms for a cationic dye, 1,1'-didodecyl-3,3,3'3'-tetramethylindocarbocyanine perchlorate (DiI), were studied at varying pH using an Agilent SB-C8 column and 80% ACN/water for six DiI concentrations ranging from 0.9 to 316 microM. The chromatograms showed increased retention and tailing from pH 1 to 5, as expected. Simulations of the chromatograms agreed well with experiment for a bi-Langmuir isotherm with weak (C8) and strong (silica) adsorption sites. The simulation parameters revealed that the number of strong adsorption sites decreases by 40% from pH 1 to 5, which indicates that the silanols causing tailing are in the SiOH, not the SiO-, form. This seems paradoxical because tailing increases with increasing pH. The simulation parameters reveal that this increased tailing from pH 1 to 5 owes to doubling of the partition coefficient for DiI to the strong adsorption site, which more than compensates for the decreasing number of sites. We attribute this increased partition coefficient to increased long-range coulombic interactions with the increasingly abundant SiO- groups at higher pH, which boosts DiI's partition coefficient for both the C8 and SiOH sites. The picture thus emerges that for DiI, higher pH causes increased tailing because the SiO- groups exacerbate tailing that actually originates from adsorption to SiOH groups.

Adsorption↗
PubMed2006

Dural tail sign in spinal meningiomas.

OBJECTIVE: To study the association between the "dural tail sign" and spinal meningiomas on MR imaging. METHODS: Retrospective review of MR examinations of all pathologically proven spinal meningiomas from 1998 to 2005 was performed. Lesions were evaluated for size, signal intensity, enhancement pattern, and presence or absence of dural tail. The dural tail length and direction in reference to the meningioma were also evaluated. RESULTS: Seven spinal meningiomas were identified in seven patients. One lesion was purely extradural, while the remaining were intradural extramedullary. Dural tail was present in four cases (57%) and its length ranged between 5 and 21 mm. The tail was seen cranial and caudal to the meningioma in three cases and only cranially in one. Coronal images were available in three cases and in two of these; the dural tail was clearly depicted. CONCLUSIONS: "Dural tail sign" is as common in spinal meningiomas as in cranial meningiomas.

Adolescent↗
PubMed2005

Receipt of the C-terminal tail from a neighboring lambda Int protomer allosterically stimulates Holliday junction resolution.

Bacteriophage lambda integrase (Int) catalyzes the integration and excision of the phage lambda chromosome into and out of the Esherichia coli host chromosome. The seven carboxy-terminal residues (C-terminal tail) of Int comprise a context-sensitive regulatory element that links catalytic function with protein multimerization and also coordinates Int functions within the multimeric recombinogenic complex. The experiments reported here show that the beta5-strand of Int is not simply a placeholder for the C-terminal tail but rather exerts its own allosteric effects on Int function in response to the incoming tail. Using a mutant integrase in which the C-terminal tail has been deleted (W350ter), we demonstrate that the C-terminal tail is required for efficient and accurate resolution of Holliday junctions by tetrameric Int. Addition of a free heptameric peptide of the same sequence as the C-terminal tail partially reverses the W350ter defects by stimulating Holliday junction resolution. The peptide also stimulates the topoisomerase function of monomeric W350ter. Single residue alterations in the peptide sequence and a mutant of the beta5 strand indicate that the observed stimulation arises from specific contacts with the beta5 strand (residues 239-243). The peptide does not stimulate binding of W350ter to its cognate DNA sites and therefore appears to recapitulate the effects of the normal C-terminal tail intermolecular contacts in wild-type Int. Models for the allosteric stimulation of Int activity by beta5 strand contacts are discussed.

Allosteric Site↗
PubMed2006

Influence of recording instrumentation on the stimulus artifact tail in the surface acquisition of somatosensory evoked potentials.

Surface recorded somatosensory evoked potentials (SEPs) are neural signals elicited by an external stimulus. In the case of electrically induced SEPs, the artifact generated by the stimulation process can severely distort the signal. The artifact is characterized by a large impulse followed by a slowly decaying tail. In some cases, the artifact tail often lasts well into the initiation of the SEP making the determination of absolute latency very difficult. While the literature often states that the recording instrumentation plays a part in the generation of this artifact tail, no firm evidence has ever been presented. In this work, comparisons are made between three instrumentation systems (BJT, JFET and CMOS) with differing input impedances in an attempt to quantify the effects on the artifact tail. The conclusions from this investigation show that there is no significant interaction between the input impedance of the recording instrumentation and the duration of the artifact tail. Each amplifier type produced results with no significant statistical differences. It was also found that while stimulation amplitude has a weak effect on the artifact tail, the greatest contribution to variation has an inter-subject origin. Consequently, it is concluded that the time constant of the artifact tail must originate from other sources that are subject dependent.

Amplifiers, Electronic↗
PubMed2005

Deleting the phosphorylated tail domain of the neurofilament heavy subunit does not alter neurofilament transport rate in vivo.

Phosphorylation of the carboxyl tail domains of the neurofilament heavy (NF-H) and middle molecular weight (NF-M) subunits has been proposed to regulate the axonal transport of neurofilaments. To test this hypothesis, we recently constructed mice lacking the extensively phosphorylated NF-H tail domain (NF-HtailDelta) and showed that the transport rate of neurofilaments in optic axons is unaltered in the absence of this domain [M.V. Rao, M.L. Garcia, Y. Miyazaki, T. Gotow, A. Yuan, S. Mattina, C.M. Ward, N.A. Calcutt, Y. Uchiyama, R.A. Nixon, D.W. Cleveland, Gene replacement in mice reveals that the heavily phosphorylated tail of neurofilament heavy subunit does not affect axonal caliber or the transit of cargoes in slow axonal transport, J. Cell Biol. 158 (2002) 681-693]. However, Shea et al. proposed that deletion of NF-H carboxyl-terminal region accelerates the transport of a subpopulation of neurofilaments based on minor differences between tail-deleted and control mice in our axonal transport analysis. Here, we present additional evidence that neurofilament transport rate is unchanged after deleting the phosphorylated NF-H tail domain, establishing unequivocally that the NF-H tail domain alone does not regulate the rate of neurofilament transport in optic axons in vivo. Possible roles for tail domains as cross-bridges between a neurofilament and its neighbors or other cytoskeletal elements is discussed.

Animals↗
PubMed2004

Adsorptive removal of phosphate from aqueous solutions using iron oxide tailings.

This study explored the feasibility of utilizing industrial waste iron oxide tailings for phosphate removal in laboratory experiments. The experimental work emphasized on the evaluation of phosphate adsorption and desorption characteristics of the tailing material. The adsorption isotherm, kinetics, pH effect and desorption were examined in batch experiments. Five isotherm models were used for data fitting. The three-parameter equations (Redlich-Peterson and Langmuir-Freundlich) showed more applicability than the two-parameter equations (Freundlich, Langmuir and Temkin). A modified equation for calculation of the separation factor using the Langmuir-Freundlich equation constants was developed. The initial phosphate adsorption on the tailings was rapid. The adsorption kinetics can be best described by either the simple Elovich or power function equation. The phosphate adsorption on the tailings tended to decrease with an increase of pH. A phosphate desorbability of approximately 13-14% was observed, and this low desorbability likely resulted from a strong bonding between the adsorbed PO(4)(3-)and iron oxides in the tailings. Column flow-through tests using both synthetic phosphate solution and liquid hog manure confirmed the phosphate removal ability of the tailings. Due to their low cost and high capability, this type of iron oxide tailings has the potential to be utilized for cost-effective removal of phosphate from wastewater.

Adsorption↗
PubMed2004

Short class I major histocompatibility complex cytoplasmic tails differing in charge detect arbiters of lateral diffusion in the plasma membrane.

Directed and Brownian movement of class I major histocompatibility complex (MHC) molecules on cell membranes is implicated in antigen presentation. Previous studies indicated that the class I MHC cytoplasmic tail imposes constraints on the molecule's diffusion. Here we used single particle tracking to study the mobility of the wild-type mouse H-2L(d) class I MHC molecule and of seven cytoplasmic tail variants. Six of the variants have cytoplasmic tails of four or seven residues (differing in net charge), and one is tailless, yet all are susceptible to confinement in membrane domains. However, truncation of the cytoplasmic tail to 0-4 residues decreases the proportion of particles exhibiting confined diffusion and increases the proportion exhibiting simple diffusion. Particularly for the truncated mutants (tail length of 0-7 residues), many of the particles have complex trajectories and do not move at a constant speed or in the same mode of diffusion throughout the observation period. Several particles of the tailless H-2L(d) mutant display a type of directed diffusion that is rarely observed for other H-2L(d) mutants. Taken together, these data show that even short cytoplasmic tails can influence markedly class I MHC mobility and that cytoplasmic tail length and sequence affect the molecule's diffusion in the membrane.

Animals↗
PubMed2000

Blockade of NMDA receptors in the nucleus accumbens elicits spontaneous tail-flicks in rats.

The open channel blocker at N-methyl-D-aspartate (NMDA) receptors, dizocilpine, stereospecifically elicited spontaneous tail-flicks in rats - a reaction similar to those elicited by other drugs (tenocyclidine, phencyclidine and ketamine) acting as open channel blockers. Their relative potencies were strongly correlated with affinities at NMDA binding sites and labeled by [3H]dizocilpine in the frontal cortex (r=0.94) and, as determined previously [Millan, M. J., Seguin, L., 1994. Chemically-diverse ligands at the glycine B site coupled to N-methyl-D-aspartate (NMDA) receptors selectively block the late phase of formalin-induced pain in mice, Neurosci. Lett., 178 (1994) 139-143], potency for eliciting antinociception (0. 93). The competitive antagonists at the NMDA receptor recognition site, (+/-)3-(2-carboxypiperazin-4-yl)-propyl-1-phosphonic acid (CPP), 4-phosphonomethyl-2-piperidine carboxylic acid (CGS19755), D, L-(E)-2-amino-4-methylphosphono-3-pentanoic acid (CGP37849) and (3E)-1-ethyl ester-2-amino-4-methyl-5-phosphono-3-pentenoic acid (CGP39551), likewise dose-dependently evoked spontaneous tail-flick. In contrast, antagonists/weak partial agonists at the coupled, glycine B site, 7-chloro-4-hydroxy-3-(3-phenoxy) phenyl-2(H)-quinolinone (L701,324), (+)-1-hydroxy-3-aminopyrrolidine-2-one ((+)-HA966), (3R, 4R)-3-amino-1-hydroxy-4-methyl-2-pyrrolidinone (L687,414), 6, 7-dichloro-1, 4-dihydro-5-nitro, 2,3 quinoxalinedione (ACEA1021) and 2-carboxy-4,6-dichloro (1H)-indole-3-propanoic acid (MDL29,951), were inactive. NMDA abolished induction of spontaneous tail-flick by CPP and CGS19755, but not by dizocilpine. Upon bilateral injection into the nucleus accumbens, dizocilpine immediately and dose-dependently elicited spontaneous tail-flick, but it was ineffective in the ventrotegmental area and striatum. Similarly, injection of CPP into the nucleus accumbens elicited spontaneous tail-flick. Neither dizocilpine nor CPP elicited spontaneous tail-flick upon administration onto lumbar spinal cord. In conclusion, a pharmacologically specific spontaneous tail-flick-response is elicited by both open channel blockers and recognition site antagonists, but not glycine B site antagonists, at NMDA receptors. Their actions, mediated in the nucleus accumbens, may be differentiated by their respective resistance and sensitivity to NMDA.

Animals↗
PubMed2003

Multiple functions of tail-anchor domains of mitochondrial outer membrane proteins.

Tail-anchored proteins form a distinct class of membrane proteins that have a single membrane anchor sequence at their C-terminus, the tail-anchor. Their N-terminal portion is exposed to the cytosol. We have studied the roles of tail-anchor domains of proteins residing in the mitochondrial outer membrane. Four distinct functions of the tail-anchor domain were identified. First, the domain mediates the targeting to mitochondria in a process that probably requires a net positive charge at the C-terminally flanking segment. Second, tail-anchor domains facilitate the insertion into the mitochondrial outer membrane. Third, the tail-anchor is responsible for the assembly of the respective protein into functional multi-subunit complexes; and fourth, tail-anchor domains can stabilize such complexes.

Amino Acid Sequence↗
PubMed1999

Secondary structure in the 5'-leader or 3'-untranslated region reduces protein yield but does not affect the functional interaction between the 5'-cap and the poly(A) tail.

The 5'-cap structure and poly(A) tail of eukaryotic mRNAs cooperate to promote translation initiation but whether this functional interaction benefits certain classes of mRNAs has not been investigated. In this study, we investigate whether a structured 5'-leader or 3'-untranslated region (UTR) affects the cap/poly(A) tail interaction. A structured leader reduced the degree to which the 5'-cap promoted translation in plant cells and inhibited translation from capped and uncapped mRNAs equally in yeast. Secondary structure within the 3'-UTR reduced translational efficiency when adjacent to the stop codon but had little effect on the cap/poly(A) tail synergy. The functional interaction between the cap and poly(A) tail was as important for an mRNA with a structured leader or 3'-UTR as it was for an unstructured mRNA in either species, suggesting that these structures can reduce translation without affecting the functional interaction between the cap and poly(A) tail. However, the loss of Xrn1p, the major 5'-->3' exoribonuclease in yeast, abolished cap-dependent translation and the functional interaction between the cap and poly(A) tail, suggesting that the cap/poly(A) tail synergy is of particular importance under conditions of active RNA turnover.

3' Untranslated Regions↗