Interactions between the Translation Machinery and Microtubules

Microtubules are components of eukaryotic cytoskeleton that are involved in the transport of various components from the nucleus to the cell periphery and back. They also act as a platform for assembly of complex molecular ensembles. Ribonucleoprotein (RNP) complexes, such as ribosomes and mRNPs, are transported over significant distances (e.g. to neuronal processes) along microtubules. The association of RNPs with microtubules and their transport along these structures are essential for compartmentalization of protein biosynthesis in cells. Microtubules greatly facilitate assembly of stress RNP granules formed by accumulation of translation machinery components during cell stress response. Microtubules are necessary for the cytoplasm-to-nucleus transport of proteins, including ribosomal proteins. At the same time, ribosomal proteins and RNA-binding proteins can influence cell mobility and cytoplasm organization by regulating microtubule dynamics. The molecular mechanisms underlying the association between the translation machinery components and microtubules have not been studied systematically; the results of such studies are mostly fragmentary. In this review, we attempt to fill this gap by summarizing and discussing the data on protein and RNA components of the translation machinery that directly interact with microtubules or microtubule motor proteins.     

Accuracy of single-plane fluoroscopy in determining relative position and orientation of total knee replacement components

The accuracy of estimating the relative pose between knee replacement components, in terms of clinical motion, is important in the study of knee joint kinematics. The objective of this study was to determine the accuracy of the single-plane fluoroscopy method in calculating the relative pose between the femoral component and the tibial component, along knee motion axes, while the components were in motion relative to one another. The kinematics of total knee replacement components were determined in vitro using two simultaneous methods: single-plane fluoroscopic shape matching and an optoelectronic motion tracking system. The largest mean differences in relative pose between the two methods for any testing condition were 2.1°, 0.3°, and 1.1° in extension, abduction, and internal rotation respectively, and 1.3, 0.9, and 1.9 mm in anterior, distal, and lateral translations, respectively. For the optimized position of the components during dynamic trials, the limits of agreement, between which 95% of differences can be expected to fall, were -2.9 to 4.5° in flexion, -0.9 to 1.5° in abduction, -2.4 to 2.1° in external rotation, -2.0 to 3.9 mm in anterior-posterior translation, -2.2 to 0.4mm in distal-proximal translation and -7.2 to 8.6mm in medial-lateral translation. These mean accuracy values and limits of agreement can be used to determine whether the shape-matching approach using single-plane fluoroscopic images is sufficiently accurate for an intended motion tracking application.     

Phosphorylation of serine-arginine rich proteins--pleiotropic effect of one type posttranslational modification

SR proteins are components of the spliceosome, a dynamic complex catalysing removal of pre-mRNA introns during splicing reaction. Recent studies have shown additional functions for SR proteins in mRNA transport and translation. Several protein kinases have been identified that can phosphorylate SR proteins. Phosphorylation is a common posttranslational modification among proteins. However in the case of SR proteins it has got a special meaning. Phosphorylation of serine residues clustered in a narrow area of RS domains affects all aspects of SR proteins functions. It influences subcellular localization and determines process in which the proteins take part.     

In vitro transport of ornithine carbamoyltransferase precursor into rat liver mitochondria using a more homologous medium

The precursor of ornithine carbamoyltransferase can be transported in vitro into rat liver mitochondria using the postmitochondrial supernatant from rat liver, a more homologous medium than the commonly used rabbit reticulocyte lysate. The transport of the precursor in the case of reticulocyte lysate requires a standard translation mixture. In the presence of the postmitochondrial supernatant the same is true. However, when the components of the translation mixture were added individually to the postmitochondrial supernatant, it was found that spermidine or spermine, at physiological concentrations, sufficed for the transport of the precursor of ornithine carbamoyltransferase. The activity of the postmitochondrial supernatant was inactivated by trypsin and slightly decreased by RNase treatment; it was not lost by dialysis or by heating at 100 degrees C.     

Adenovirus E1B proteins are required for accumulation of late viral mRNA and for effects on cellular mRNA translation and transport.

Late in adenovirus infection, large amounts of viral mRNA accumulate while cell mRNA transport and translation decrease. Viruses deleted in the E1B region of type 5 adenovirus do not produce the same outcome: (i) viral mRNA synthesis by the mutants is normal, delivery to the cytoplasm is 50 to 75% of normal, but steady-state levels of viral mRNA are decreased 10-fold; (ii) cell mRNA synthesis and transport continue normally in the mutant virus-infected cell; and (iii) translation of preexisting cell mRNA which is disrupted in wild-type infection remains normal in mutant-virus-infected cells. Thus E1B proteins are required for accumulation of virus mRNA and for induction of the failure of host cell mRNA transport and translation. If a single function is involved, by inference the transport and some aspect of translation of mRNAs could be linked.     

Type-IV Pilus Deformation Can Explain Retraction Behavior

Polymeric filament like type IV Pilus (TFP) can transfer forces in excess of 100 pN during their retraction before stalling, powering surface translocation(twitching). Single TFP level experiments have shown remarkable nonlinearity in the retraction behavior influenced by the external load as well as levels of PilT molecular motor protein. This includes reversal of motion near stall forces when the concentration of the PilT protein is loweblack significantly. In order to explain this behavior, we analyze the coupling of TFP elasticity and interfacial behavior with PilT kinetics. We model retraction as reaction controlled and elongation as transport controlled process. The reaction rates vary with TFP deformation which is modeled as a compound elastic body consisting of multiple helical strands under axial load. Elongation is controlled by monomer transport which suffer entrapment due to excess PilT in the cell periplasm. Our analysis shows excellent agreement with a host of experimental observations and we present a possible biophysical relevance of model parameters through a mechano-chemical stall force map.     

The interaction of wheat germ tyrosyl-tRNA synthetase and the tRNA-like end of brome mosaic virus RNA has no effect on in vitro viral protein synthesis and on in vitro encapsidation.

The effect of aminoacylation of the tRNA-like end of brome mosaic virus RNA during in vitro protein synthesis and in vitro viral encapsidation was investigated. The components of the homologous system were: BMV RNA, wheat germ cell-free protein synthesizing system and pure tyrosyl-tRNA synthetase from wheat germ. During in vitro protein synthesis directed with tyrosylated as well as non-tyrosylated BMV RNA, no differences were observed in the amount and in the class of polypeptides formed neither in the velocity of the translation reaction. Excess active TyrRS was added during in vitro translation, without modifying the translation efficiency. BMV RNA and active TyrRS were preincubated prior to translation in order to interact without the translation system components and then subjected to translation in vitro. Similar results were obtained when BMV RNA was preincubated with inactive TyrRS or BSA. These results indicate that the aminoacylation of BMV RNA has no pronounced effect on viral protein synthesis in vitro. During BMV RNA encapsidation either tyrosylated or non-tyrosylated BMV RNA 4 could be encapsidated in a similar way.     

Comparison of Efficency of Translation Between a Deformable Swimmer Versus a Rigid Body in a Bounded Fluid Domain: Consequences for Subcellular Transport

In this paper, we compare the translation efficiencies of a deformable circle that swims by means of low amplitude periodic tangential surface waves versus a rigid circle, moving in a bounded fluid domain. The swimmer is found to be much more efficient than the rigid body. We believe that this result gives some support to the active hypothesis of subcellular transport, where it is supposed that the organelle can generate by itself a propulsive flux, (by changes of form or metabolic activities) instead of just being carried by the motion of an external agent, like a molecular motor.     

Motion parallax contribution to perception of self-motion and depth

The object of this study is to mathematically specify important characteristics of visual flow during translation of the eye for the perception of depth and self-motion. We address various strategies by which the central nervous system may estimate self-motion and depth from motion parallax, using equations for the visual velocity field generated by translation of the eye through space. Our results focus on information provided by the movement and deformation of three-dimensional objects and on local flow behavior around a fixated point. All of these issues are addressed mathematically in terms of definite equations for the optic flow. This formal characterization of the visual information presented to the observer is then considered in parallel with other sensory cues to self-motion in order to see how these contribute to the effective use of visual motion parallax, and how parallactic flow can, conversely, contribute to the sense of self-motion. This article will focus on a central case, for understanding of motion parallax in spacious real-world environments, of monocular visual cues observable during pure horizontal translation of the eye through a stationary environment. We suggest that the global optokinetic stimulus associated with visual motion parallax must converge in significant fashion with vestibular and proprioceptive pathways that carry signals related to self-motion. Suggestions of experiments to test some of the predictions of this study are made.     

Head tilt–translation combinations distinguished at the level of neurons

Angular and linear accelerations of the head occur throughout everyday life, whether from external forces such as in a vehicle or from volitional head movements. The relative timing of the angular and linear components of motion differs depending on the movement. The inner ear detects the angular and linear components with its semicircular canals and otolith organs, respectively, and secondary neurons in the vestibular nuclei receive input from these vestibular organs. Many secondary neurons receive both angular and linear input. Linear information alone does not distinguish between translational linear acceleration and angular tilt, with its gravity-induced change in the linear acceleration vector. Instead, motions are thought to be distinguished by use of both angular and linear information. However, for combined motions, composed of angular tilt and linear translation, the infinite range of possible relative timing of the angular and linear components gives an infinite set of motions among which to distinguish the various types of movement. The present research focuses on motions consisting of angular tilt and horizontal translation, both sinusoidal, where the relative timing, i.e. phase, of the tilt and translation can take any value in the range −180° to 180°. The results show how hypothetical neurons receiving convergent input can distinguish tilt from translation, and that each of these neurons has a preferred combined motion, to which the neuron responds maximally. Also shown are the values of angular and linear response amplitudes and phases that can cause a neuron to be tilt-only or translation-only. Such neurons turn out to be sufficient for distinguishing between combined motions, with all of the possible relative angular–linear phases. Combinations of other neurons, as well, are shown to distinguish motions. Relative response phases and in-phase firing-rate modulation are the key to identifying specific motions from within this infinite set of combined motions.     

Separating brain motion into rigid body displacement and deformation under low-severity impacts

The relative motion of the brain with respect to the skull has been widely studied to investigate brain injury mechanisms under impacts, but the motion patterns are not yet thoroughly understood. This work analyzes brain motion patterns using the most recent and advanced experimental relative brain/skull motion data collected under low-severity impacts. With a minimum total pseudo-strain energy, the closed-form solutions for rigid body translation and rotation were obtained by matching measured neutral density target (NDT) positions with initial NDT positions. The brain motion was thus separated into rigid body displacement and deformation. The results show that the brain has nearly pure rigid body displacement at low impact speed. As the impact becomes more severe, the increased brain motion primarily is due to deformation, while the rigid body displacement is limited in magnitude for both translation and rotation. Under low-severity impacts in the sagittal plane, the rigid body brain translation has a magnitude of 4-5 mm, and the whole brain rotation is on the order of +/-5 degrees.     

An integrated fluid–structure interaction and thrombosis model for type B aortic dissection

False lumen thrombosis (FLT) in type B aortic dissection has been associated with the progression of dissection and treatment outcome. Existing computational models mostly assume rigid wall behavior which ignores the effect of flap motion on flow and thrombus formation within the FL. In this study, we have combined a fully coupled fluid–structure interaction (FSI) approach with a shear-driven thrombosis model described by a series of convection–diffusion reaction equations. The integrated FSI-thrombosis model has been applied to an idealized dissection geometry to investigate the interaction between vessel wall motion and growing thrombus. Our simulation results show that wall compliance and flap motion can influence the progression of FLT. The main difference between the rigid and FSI models is the continuous development of vortices near the tears caused by drastic flap motion up to 4.45 mm. Flap-induced high shear stress and shear rates around tears help to transport activated platelets further to the neighboring region, thus speeding up thrombus formation during the accelerated phase in the FSI models. Reducing flap mobility by increasing the Young’s modulus of the flap slows down the thrombus growth. Compared to the rigid model, the predicted thrombus volume is 25% larger using the FSI-thrombosis model with a relatively mobile flap. Furthermore, our FSI-thrombosis model can capture the gradual effect of thrombus growth on the flow field, leading to flow obstruction in the FL, increased blood viscosity and reduced flap motion. This model is a step closer toward simulating realistic thrombus growth in aortic dissection, by taking into account the effect of intimal flap and vessel wall motion.

     

The dynamics of mammalian P body transport, assembly, and disassembly in vivo

Exported mRNAs are targeted for translation or can undergo degradation by several decay mechanisms. The 5′→3′ degradation machinery localizes to cytoplasmic P bodies (PBs). We followed the dynamic properties of PBs in vivo and investigated the mechanism by which PBs scan the cytoplasm. Using proteins of the decapping machinery, we asked whether PBs actively scan the cytoplasm or whether a diffusion-based mechanism is sufficient. Live-cell imaging showed that PBs were anchored mainly to microtubules. Quantitative single-particle tracking demonstrated that most PBs exhibited spatially confined motion dependent on microtubule motion, whereas stationary PB pairs were identified at the centrosome. Some PBs translocated in long-range movements on microtubules. PB mobility was compared with mitochondria, endoplasmic reticulum, peroxisomes, SMN bodies, and stress granules, and diffusion coefficients were calculated. Disruption of the microtubule network caused a significant reduction in PB mobility together with an induction of PB assembly. However, FRAP measurements showed that the dynamic flux of assembled PB components was not affected by such treatments. FRAP analysis showed that the decapping enzyme Dcp2 is a nondynamic PB core protein, whereas Dcp1 proteins continuously exchanged with the cytoplasm. This study reveals the mechanism of PB transport, and it demonstrates how PB assembly and disassembly integrate with the presence of an intact cytoskeleton.     

DNA sequence of the porcine α-lactalbumin 5' flanking region and single-base polymorphisms within this region

The 5' flanking region of the α-lactalbumin (α-LA) gene was sequenced for the Duroc, Yorkshire and Meishan breeds of swine to identify potential sequence variants within this regulatory region of the porcine α-LA gene. The sequenced region of the gene encompasses 391 bp 5' of the translation start site to 11 bp 3' of the translation start site. Within this sequence of the porcine α-LA gene two single-base pair differences were detected. One variant occurs at position – 178 and the other at position – 235 from the translation start site. Each of the variations can be detected by a restriction fragment length polymorphism within a polymerase chain reaction amplified product. The polymorphisms at the – 178 and – 235 positions appear to be genetically linked in the animals that have been analysed.     

Drag of the Cytosol as a Transport Mechanism in Neurons

Axonal transport is typically divided into two components, which can be distinguished by their mean velocity. The fast component includes steady trafficking of different organelles and vesicles actively transported by motor proteins. The slow component comprises nonmembranous materials that undergo infrequent bidirectional motion. The underlying mechanism of slow axonal transport has been under debate during the past three decades. We propose a simple displacement mechanism that may be central for the distribution of molecules not carried by vesicles. It relies on the cytoplasmic drag induced by organelle movement and readily accounts for key experimental observations pertaining to slow-component transport. The induced cytoplasmic drag is predicted to depend mainly on the distribution of microtubules in the axon and the organelle transport rate.