Bidirectional transport and pulsing states in a multi-lane ASEP model

In this paper, we introduce an ASEP-like transport model for bidirectional motion of particles on a multi-lane lattice. The model is motivated by {\em in vivo} experiments on organelle motility along a microtubule (MT), consisting of thirteen protofilaments, where particles are propelled by molecular motors (dynein and kinesin). In the model, organelles (particles) can switch directions of motion due to "tug-of-war" events between counteracting motors. Collisions of particles on the same lane can be cleared by switching to adjacent protofilaments (lane changes). We analyze transport properties of the model with no-flux boundary conditions at one end of a MT ("plus-end" or tip). We show that the ability of lane changes can affect the transport efficiency and the particle-direction change rate obtained from experiments is close to optimal in order to achieve efficient motor and organelle transport in a living cell. In particular, we find a nonlinear scaling of the mean {\em tip size} (the number of particles accumulated at the tip) with injection rate and an associated phase transition leading to {\em pulsing states} characterized by periodic filling and emptying of the system.Comment: 11 figure

The fungus Ustilago maydis and humans share disease-related proteins that are not found in Saccharomyces cerevisiae

<p>Abstract</p> <p>Background</p> <p>The corn smut fungus <it>Ustilago maydis </it>is a well-established model system for molecular phytopathology. In addition, it recently became evident that <it>U. maydis </it>and humans share proteins and cellular processes that are not found in the standard fungal model <it>Saccharomyces cerevisiae</it>. This prompted us to do a comparative analysis of the predicted proteome of <it>U. maydis</it>, <it>S. cerevisiae </it>and humans.</p> <p>Results</p> <p>At a cut off at 20% identity over protein length, all three organisms share 1738 proteins, whereas both fungi share only 541 conserved proteins. Despite the evolutionary distance between <it>U. maydis </it>and humans, 777 proteins were shared. When applying a more stringent criterion (≥ 20% identity with a homologue in one organism over at least 50 amino acids and ≥ 10% less in the other organism), we found 681 proteins for the comparison of <it>U. maydis </it>and humans, whereas the both fungi share only 622 fungal specific proteins. Finally, we found that <it>S. cerevisiae </it>and humans shared 312 proteins. In the <it>U. maydis </it>to <it>H. sapiens </it>homology set 454 proteins are functionally classified and 42 proteins are related to serious human diseases. However, a large portion of 222 proteins are of unknown function.</p> <p>Conclusion</p> <p>The fungus <it>U. maydis </it>has a long history of being a model system for understanding DNA recombination and repair, as well as molecular plant pathology. The identification of functionally un-characterized genes that are conserved in humans and <it>U. maydis </it>opens the door for experimental work, which promises new insight in the cell biology of the mammalian cell.</p

Die Bedeutung von Myo5 für das polare Wachstum, die pathogene Entwicklung und den Transport polarer Chitinsynthasen in Ustilago maydis

Der phytopathogene Pilz Ustilago maydis ist der Erreger des Maisbeulenbrandes. Die Bildung des infektiösen dikaryotischen Filaments setzt die Fusion zweier kompatibler Sporidien voraus, die stimuliert durch das Pheromon des Partners Konjugationshyphen ausbilden, aufeinander zu wachsen und miteinander fusionieren. Sowohl für den Kreuzungsprozess als auch für die erfolgreiche Infektion der Wirtspflanze ist die Fähigkeit des Pilzes, polar zu wachsen, von essentieller Bedeutung. Polares Wachstum erfordert die gerichtete Anlieferung von Wachstums- und Zellwandkomponenten entlang des Cytoskeletts zur Wachstumsspitze hin. In der vorliegenden Arbeit konnte gezeigt werden, dass das Klasse V Myosin, Myo5, für verschiedene Stadien des Pilzes während seines sexuellen Lebenszyklus von enormer Bedeutung ist. Myo5 ist essentiell für die erfolgreiche Perzeption des Pheromons und die Ausbildung von Konjugationshyphen. Auch das Wachstum dikaryotischer Hyphen ist in myo5ts-Mutanten gestört. Zudem zeigten myo5ts-Infektionshyphen deutliche Störungen des polaren Wachstums während der frühen Infektionsphase, was sich in der Ausbildung geschwollene Hyphenverzweigungen äußerte, und sie induzierten bereits bei permissiver Temperatur nur bei 2,7% der Pflanzen Tumore. Aufgrund der aus Vorversuchen resultierenden Erkenntnisse wurden Chitinsynthasen als mögliche ?Cargos? von Myo5 in Betracht gezogen und näher untersucht. Das Genom von U. maydis kodiert für sieben Chitinsynthasen (Chs1-7) und eine Myosin-Chitinsynthase (Mcs1). Sowohl die Phänotypen der Chitinsynthase-Deletionsstämme wurden näher analysiert, als auch in vivo Lokalisationsstudien der Chitinsynthasen durchgeführt. Dabei zeigte sich, dass Dchs5- und auch Dchs7-Zellen ähnliche Zelltrennungsdefekte wie Dmyo5-Zellen sowie Störungen in der Ausbildung von Konjugationshyphen aufwiesen. Zudem führte die Deletion von chs7 zu einer starken Beeinträchtigung der Filamentbildung auf aktivkohlehaltigem Medium und der Pathogenität. Die Deletion von chs6 und mcs1 störte die Filamentbildung kompatibler Stämme nicht, resultierte allerdings in einer völligen Apathogenität. Ähnlich wie Myo5 lokalisierten die vier Chitinsynthasen Chs5, Chs6, Chs7 und Mcs1 in der Spitze wachsender Sporidien. Inhibitorversuche ergaben, dass die Lokalisation dieser polaren Chitinsynthasen von Aktin abhängt. Untersuchungen zur Lokalisation von Chs5, Chs6, Chs7 und Mcs1 in myo5ts-Mutanten zeigten eine deutliche Fehlverteilung von Chs7 in myo5ts-Mutanten nach einstündiger Inkubation bei restriktiver Temperatur. Durch den neu etabliertem in vivo Aktinmarker Fim1GFP konnte eine Störung des Aktin-Cytoskeletts als Ursache ausgeschlossen werden. Sowohl die phänotypischen Analysen als auch die Lokalisations- und Inhibitorstudien weisen deutlich auf eine Beteiligung von Myo5 an der Lokalisation von Chs7 hin

Motor-mediated bidirectional transport along an antipolar microtubule bundle: A mathematical model

Copyright © 2013 American Physical SocietyLong-distance bidirectional transport of organelles depends on the coordinated motion of various motor proteins on the cytoskeleton. Recent quantitative live cell imaging in the elongated hyphal cells of Ustilago maydis has demonstrated that long-range motility of motors and their endosomal cargo occurs on unipolar microtubules (MTs) near the extremities of the cell. These MTs are bundled into antipolar bundles within the central part of the cell. Dynein and kinesin-3 motors coordinate their activity to move early endosomes (EEs) in a bidirectional fashion where dynein drives motility towards MT minus ends and kinesin towards MT plus ends. Although this means that one can easily assign the drivers of bidirectional motion in the unipolar section, the bipolar orientations in the bundle mean that it is possible for either motor to drive motion in either direction. In this paper we use a multilane asymmetric simple exclusion process modeling approach to simulate and investigate phases of bidirectional motility in a minimal model of an antipolar MT bundle. In our model, EE cargos (particles) change direction on each MT with a turning rate Ω and there is switching between MTs in the bundle at the minus ends. At these ends, particles can hop between MTs with rate q1 on passing from a unipolar to a bipolar section (the obstacle-induced switching rate) or q2 on passing in the other direction (the end-induced switching rate). By a combination of numerical simulations and mean-field approximations, we investigate the distribution of particles along the MTs for different values of these parameters and of Θ, the overall density of particles within this closed system. We find that even if Θ is low, the system can exhibit a variety of phases with shocks in the density profiles near plus and minus ends caused by queuing of particles. We discuss how the parameters influence the type of particle that dominates active transport in the bundle

Queueing induced by bidirectional motor motion near the end of a microtubule

© 2010 The American Physical SocietyRecent live observations of motors in long-range microtubule (MT) dependent transport in the fungus Ustilago maydis have reported bidirectional motion of dynein and an accumulation of the motors at the polymerization-active (the plus-end) of the microtubule. Quantitative data derived from in vivo observation of dynein has enabled us to develop an accurate, quantitatively-valid asymmetric simple exclusion process (ASEP) model that describes the coordinated motion of anterograde and retrograde motors sharing a single oriented microtubule. We give approximate expressions for the size and distribution of the accumulation, and discuss queueing properties for motors entering this accumulation. We show for this ASEP model, that the mean accumulation can be modeled as an M/M/∞ queue that is Poisson distributed with mean F(arr)/p(d), where F(arr) is the flux of motors that arrives at the tip and p(d) is the rate at which individual motors change direction from anterograde to retrograde motion. Deviations from this can in principle be used to gain information about other processes at work in the accumulation. Furthermore, our work is a significant step toward a mathematical description of the complex interactions of motors in cellular long-range transport of organelles

New insights into the peroxisomal protein inventory: Acyl-CoA oxidases and -dehydrogenases are an ancient feature of peroxisomes

Journal ArticleCopyright © 2014 Elsevier B.V. All rights reserved.Peroxisomes are ubiquitous organelles which participate in a variety of essential biochemical pathways. An intimate interrelationship between peroxisomes and mitochondria is emerging in mammals, where both organelles cooperate in fatty acid β-oxidation and cellular lipid homeostasis. As mitochondrial fatty acid β-oxidation is lacking in yeast and plants, suitable genetically accessible model systems to study this interrelationship are scarce. Here, we propose the filamentous fungus Ustilago maydis as a suitable model for those studies. We combined molecular cell biology, bioinformatics and phylogenetic analyses and provide the first comprehensive inventory of U. maydis peroxisomal proteins and pathways. Studies with a peroxisome-deficient Δpex3 mutant revealed the existence of parallel and complex, cooperative β-oxidation pathways in peroxisomes and mitochondria, mimicking the situation in mammals. Furthermore, we provide evidence that acyl-CoA dehydrogenases (ACADs) are bona fide peroxisomal proteins in fungi and mammals and together with acyl-CoA oxidases (ACOX) belong to the basic enzymatic repertoire of peroxisomes. A genome comparison with baker's yeast and human gained new insights into the basic peroxisomal protein inventory shared by humans and fungi and revealed novel peroxisomal proteins and functions in U. maydis. The importance of our findings for the evolution and function of the complex interrelationship between peroxisomes and mitochondria in fatty acid β-oxidation is discussed.Portuguese Foundation for Science and Technology (FCT)FEDER/COMPETEBBSRCCRUP/Treaty of Windso