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Thesis (Ph. D.)--Hong Kong University of Science and Technology, 2003. / Includes bibliographical references (leaves 133-154). Also available in electronic version. Access restricted to campus users.

Thesis (Ph. D.)--Ohio University, March, 2004. / Includes bibliographical references (leaves 131-146).

Thesis (Ph. D. in Cell and Developmental Biology)--Vanderbilt University, Dec. 2009. / Title from title screen. Includes bibliographical references.

Thesis (Ph. D.)--Oregon State University, 2011. / Printout. Includes bibliographical references (leaves 136-149). Also available on the World Wide Web.

Thesis (Ph.D.)--Ohio University, August, 2005. / Includes bibliographical references (leaves 130-156)

Within the past thirty years, the discovery and characterization of the microtubule-associated motor proteins, kinesins and cytoplasmic dynein, has radically expanded our understanding of intracellular trafficking and motile phenomena. Nevertheless, the mechanisms by which eukaryotic cells integrate motor functionality and cargo interactions over multiple subcellular domains in a spatiotemporally controlled way remain largely mysterious. During transport within the neuronal axon, dynein and the kinesins run in opposite directions along uniformly polarized microtubule tracks, so that each motor must switch between active transport and being, itself, a cargo in order to be properly positioned and carry out its function. The axon thus represents a model system in which to study the regulatory mechanisms governing intracellular transport, especially under conditions when it must be modulated in response to changing environmental cues, such as during axon outgrowth and development. Recently, the localization of certain messenger RNAs and their local translation to yield protein has emerged as a critical process for the development of axons and other neuronal compartments. I observed that transcripts encoding the dynein cofactors Lis1 and dynactin are among those localized to axons, so I hypothesized that stimulus-dependent changes in axonal transport may occur via local synthesis of dynein cofactors. In these studies, I have shown that different conditions of nerve growth factor signaling on developing axons trigger acute changes in the transport of various axonal cargoes, contemporaneous with rapid translational activation and production of Lis1 and dynactin’s main subunit, p150Glued, within the axons themselves. Differential synthesis of these cofactors in axons was confirmed to be required for the observed stimulus-dependent transport changes, which were completely prevented by axon-specific pharmacologic inhibition of protein synthesis or RNA interference targeted against Lis1 and p150Glued. In fact, Lis1 was, in an apparent paradox, locally synthesized in response to both nerve growth factor stimulation and withdrawal. I demonstrated that this is due to the fact that Lis1 is produced from a heterogeneous population of localized transcripts, differentiated chiefly by whether they interact with the RNA-binding protein APC. Preventing the binding of APC to Lis1 transcripts thus inhibited axonal synthesis of Lis1 and its resultant transport effects under conditions of nerve growth factor stimulation, while having no bearing on the similar phenomena seen during nerve growth factor withdrawal. This demonstrates that association with RNA-binding proteins can functionally distinguish sub-populations of localized messenger RNAs, which, in turn, provides a foundation for mechanistically understanding how localized protein synthesis is coupled to specific stimuli. Axonally synthesized Lis1 also was shown to have a particular role in mediating transport of a retrograde death signal originating in nerve growth factor-deprived axons, as neurons exhibited greatly reduced cell death when axonal synthesis of Lis1 was blocked. Through the application of pharmacologic agents inhibiting different steps in the propagation of this pro-apoptotic signal, I established that the signal depends upon effective endocytosis and the activity of glycogen synthase kinase 3β. It is therefore likely that the retrogradely transported signaling cargo in question is a glycogen synthase kinase 3β-containing endosome or multivesicular body—a type of large cargo consistent with Lis1’s known role in adapting the dynein motor for high-load transport. Preliminary results further indicate that axons exposed to another type of degenerative stress, in the form of toxic amyloid-β oligomers, may also employ local synthesis of Lis1 as a means of regulating transport and survival signaling. These findings establish a previously undescribed mechanism of regulating dynein activity and cargo interactions through local synthesis of its cofactors, allowing for rapid responses to environmental cues and stimuli that are especially relevant during the development of the nervous system. In addition to illustrating a regulatory principle that may be generally applicable to subcellular compartments throughout polarized cells, these studies provide new insights into intracellular transport disruptions that occur in lissencephaly, neurodegeneration, and other human disease states.

The cytoskeletal molecular motors kinesin-1 and cytoplasmic dynein drive many diverse functions within eukaryotic cells. They are responsible for numerous spatially and temporally dependent intracellular processes crucial for cellular activity, including cytokinesis, maintenance of sub-cellular organization and the transport of myriad cargos along microtubule tracks. Cytoplasmic dynein and kinesin-1 are processive, but opposite polarity, homodimeric motors; they each can take hundreds of thousands of consecutive steps, but do so in opposite directions along their microtubule tracks. These steps are fueled by the binding and hydrolysis of ATP within the homodimer's two identical protomers. Individual motors achieve their processivity by maintaining asynchrony between the stepping cycles of each protomer, insuring that at least one protomer always maintains contact with the track. How dynein coordinates the asynchronous stepping activity of its protomers is unknown. We developed a versatile method for assembling Saccharomyces cerevisiae dynein heterodimers, using complementary DNA oligonucleotides covalently linked to dynein monomers labeled with different organic fluorophores. Using two-color, single-molecule microscopy and high-precision, two-dimensional tracking, we found that dynein has a highly variable stepping pattern that is distinct from all other processive cytoskeletal motors, which use "hand-over-hand" mechanisms. Uniquely, dynein stepping is stochastic when its two motor domains are close together. However, coordination emerges as the distance between motor domains increases, implying that a tension-based mechanism governs these steps. Many cellular cargos demonstrate bidirectional movement due to the presence of ensembles of both cytoplasmic dynein and kinesin-1. To investigate the mechanisms that coordinate the interactions between motors within an ensemble, we constructed programmable synthetic cargos using three-dimensional DNA origami. This system enables varying numbers of DNA oligonucleotide-linked motors to be attached to the synthetic cargo, allowing for control of motor type, number, spacing, and orientation in vitro. In ensembles of one to seven identical- polarity motors, we found that motor number had minimal effect on directional velocity, whereas ensembles of opposite-polarity motors engaged in a tug-of-war resolvable by disengaging one motor species.

Undergraduate honors paper--Mount Holyoke College, 2008. Dept of Biological Sciences. / Includes bibliographical references (leaves 57-59).

Cytoplasmic dynein is a molecular motor that moves cargos along microtubules. Dynein, together with its large co-factor dynactin, is responsible for the vast majority of traffic towards the centre of the cell. The largest subunit of the dynein complex is called the dynein heavy chain (DHC). The DHC includes a C-terminal motor domain, which converts ATP hydrolysis into mechanical force, an N-terminal tail domain, and a flexible linker domain to join the two together. An intermediate chain (DIC) and light intermediate chain (DLIC) bind directly to the DHC tail, while light chains (DLCs) bind to the DIC. This tail complex is important for both cargo binding as well as homodimerisation of the DHC, which is necessary for processive movement. Previous studies suggest that the DLCs play an important role in homodimerisation, but it remains unclear how else the DHCs are held together. Using S. cerevisiae as a model system, I co-expressed all four dynein subunits and purified functional dynein motors. In this background, I found that truncating the DHC to include only the first 1004 residues (out of the total 4092) eliminates the motor domain as well as the flexible linker domain, while preserving binding to the DIC, DLIC and DLC. However, truncating just another 50 residues off of the C-terminus led to a loss of all accessory subunits. I developed a protocol for expressing and purifying large quantities of the 1004 residue construct, thus I provide the first description of a recombinant dynein tail domain. Using negative stain electron microscopy (EM), I also present the first 3D structural information for the tail region of the cytoplasmic dynein motor. I then describe a construct including only the first 557 residues of the DHC, which dimerises despite not being able to bind any of the other subunits. I present a crystal structure of this smaller DHC fragment, which shows that the N-terminal 180 residues of the DHC constitute an intricate dimerisation domain made up of a β-sheet sandwiched between α-helices. Not only is this the first crystal structure of any part of the DHC N-terminus, but it reveals a previously undocumented dimerisation domain within the DHC itself. Furthermore, information garnered from this crystal structure allowed for interpretation of a recent cryo-EM structure of a triple complex containing the dynein tail, dynactin and the cargo adaptor BICD2 (TDB) that was solved by my colleagues in the Carter group. Only by docking the DHC N-terminus crystal structure within the TDB EM density did it become clear that the N-terminus of the DHC is responsible for the majority of the contacts the dynein tail makes with both dynactin and BICD2. Therefore the work that I present here sheds new light on the unexpected importance of the DHC N-terminus and allows two important conclusions to be made. First, the N-terminal 180 residues of the DHC constitute a dimerisation domain of its own. Second, the next ~400 residues of the DHC form a domain that plays a key role in the complex interface between dynein, dynactin and BICD2.