Dimitris Liakopoulos

A novel protein modification pathway related to the ubiquitin system

Ubiquitin conjugation is known to target protein substrates primarily to degradation by the proteasome or via the endocytic route. Here we describe a novel protein modification pathway in yeast which mediates the conjugation of RUB1, a ubiquitin‐like protein displaying 53% amino acid identity to ubiquitin. We show that RUB1 conjugation requires at least three proteins in vivo. ULA1 and UBA3 are related to the N‐ and C‐terminal domains of the E1 ubiquitin‐activating enzyme, respectively, and together fulfil E1‐like functions for RUB1 activation. RUB1 conjugation also requires UBC12, a protein related to E2 ubiquitin‐conjugating enzymes, which functions analogously to E2 enzymes in RUB1–protein conjugate formation. Conjugation of RUB1 is not essential for normal cell growth and appears to be selective for a small set of substrates. Remarkably, CDC53/cullin, a common subunit of the multifunctional SCF ubiquitin ligase, was found to be a major substrate for RUB1 conjugation. This suggests that the RUB1 conjugation pathway is functionally affiliated to the ubiquitin–proteasome system and may play a regulatory role.

Regulation of Mitotic Spindle Asymmetry by SUMO and the Spindle-Assembly Checkpoint in Yeast

During mitosis, the kinetochore microtubules capture and segregate chromosomes, and the astral microtubules position the spindle within the cell. Although the spindle is symmetric, proper positioning of the spindle in asymmetrically dividing cells generally correlates with the formation of morphologically and structurally distinct asters [1]. In budding yeast, the spindle-orientation proteins Kar9 and dynein decorate only one aster of the metaphase spindle and direct it toward the bud [2, 3]. The mechanisms controlling the distribution of Kar9 and dynein remain unclear. Here, we show that SUMO regulates astral-microtubule function in at least two ways. First, Kar9 was sumoylated in vivo. Sumoylation and Cdk1-dependent phosphorylation of Kar9 independently promoted Kar9 asymmetry on the spindle. Second, proper regulation of kinetochore function by SUMO was also required for Kar9 asymmetry. Indeed, activation of the spindle-assembly checkpoint (SAC) due to SUMO and kinetochore defects promoted symmetric redistribution of Kar9 in a Mad2-dependent manner. The control of Kar9 distribution by the SAC was independent of Kar9 sumoylation and phosphorylation. Together, our data reveal that three independent mechanisms contribute to Kar9 asymmetry: Cdk1-dependent phosphorylation, sumoylation, and SAC signaling. Hence, the two seemingly independent spindle domains, kinetochores and astral microtubules, function in a tightly coordinated fashion.

Molecular mechanisms in spindle positioning: structures and new concepts

Coordination of cell cleavage with respect to cell geometry, cell polarity and neighboring tissues is critical for tissue maintenance, malignant transformation and metastasis. The position of the mitotic spindle within the cell determines where cell cleavage occurs. Spindle positioning is often mediated through capture of astral microtubules by motor proteins at the cell cortex. Recently, the core dynein anchor complex has been structurally resolved. Junctional complexes were shown to provide additional capture sites for astral microtubules in proliferating tissues. Finally, latest studies show that signals from centrosomes control spindle positioning and propose novel concepts for generation of centrosome identity.

Ubiquitylation Regulates Interactions of Astral Microtubules with the Cleavage Apparatus

BACKGROUND Correct positioning of the mitotic spindle relative to the cleavage apparatus is crucial for successful mitosis. In budding yeast, the Adenomatous Polyposis Coli-related protein Kar9, yeast EB1, and Myo2, a type V myosin, mediate positioning of the mitotic spindle close to the septin-anchored cleavage apparatus at the bud neck. RESULTS We find that Kar9 is ubiquitylated and degraded by the proteasome. Ubiquitylation requires the ubiquitin-conjugating enzymes Ubc1 and Ubc4 and phosphorylation of Kar9 by yeast Cdk1. Importantly, Kar9 ubiquitylation and degradation depend on an intact cleavage apparatus. Kar9 is stabilized in septin mutant cells or cells lacking the bud neck formin Bnr1, but not in the bud formin Bni1 or the actomyosin ring. Transport of Kar9 to the bud neck by Myo2 is also required for Kar9 degradation. Abrogation of Kar9 phosphorylation and ubiquitylation increases interactions of astral microtubules (aMTs) with the bud neck and causes spindle mispositioning. Photoconversion experiments showed that Kar9 association with aMTs is stable. CONCLUSIONS We propose that ubiquitylation controls interactions of aMTs with the cleavage apparatus through localized disassembly of Kar9 complexes.

Role of spindle asymmetry in cellular dynamics.

The mitotic spindle is mostly perceived as a symmetric structure. However, in many cell divisions, the two poles of the spindle organize asters with different dynamics, associate with different biomolecules or subcellular domains, and perform different functions. In this chapter, we describe some of the most prominent examples of spindle asymmetry. These are encountered during cell-cycle progression in budding and fission yeast and during asymmetric cell divisions of stem cells and embryos. We analyze the molecular mechanisms that lead to generation of spindle asymmetry and discuss the importance of spindle-pole differentiation for the correct outcome of cell division.

Characterization of ubiquitin genes and -transcripts and demonstration of a ubiquitin-conjugating system in Entamoeba histolytica☆

We have investigated the genomic organization of Entamoeba histolytica ubiquitin and looked for the occurrence of a ubiquitin-conjugating system in this organism. Southern blots indicated the presence of > or = 5 ubiquitin-coding regions. One of these, EhUBI1, was cloned and sequenced and found to correspond to a monoubiquitin gene; as shown by a polymerase chain reaction, E. histolytica lacked polyubiquitin genes altogether. Blots of poly(A)+ RNA from exponentially-growing trophozoite cultures exhibited five ubiquitin transcripts, the most prominent and smallest of which corresponded to EhUBI1 mRNA. Expression of the ubiquitin genes was not influenced by heat shock. Although the predicted amino acid sequence of the ubiquitin from E. histolytica differs significantly (in 7-9 amino acid residues) from that of yeast and animals, expression of the coding sequence of EhUBI1 suppressed the heat-sensitive phenotype of a polyubiquitin gene-deficient yeast mutant. In correlation, trophozoite extract catalyzed an ATP-dependent conjugation of radioiodinated bovine ubiquitin to trophozoite proteins. The latter data indicate that E. histolytica contains a functional ubiquitin-conjugating system.

An auxiliary, membrane-based mechanism for nuclear migration in budding yeast.

The preanaphase nucleus of budding yeast deforms and builds protrusions into the bud. Formation of the nuclear protrusions requires membrane growth and DNA replication. Nuclear protrusions anchor the nuclear envelope to the cortical ER in an actin- and exocyst-dependent manner, facilitating spindle positioning relative to the cleavage apparatus.

Kinesin Kip2 enhances microtubule growth in vitro through length-dependent feedback on polymerization and catastrophe

The size and position of mitotic spindles is determined by the lengths of their constituent microtubules. Regulation of microtubule length requires feedback to set the balance between growth and shrinkage. Whereas negative feedback mechanisms for microtubule length control, based on depolymerizing kinesins and severing proteins, have been studied extensively, positive feedback mechanisms are not known. Here, we report that the budding yeast kinesin Kip2 is a microtubule polymerase and catastrophe inhibitor in vitro that uses its processive motor activity as part of a feedback loop to further promote microtubule growth. Positive feedback arises because longer microtubules bind more motors, which walk to the ends where they reinforce growth and inhibit catastrophe. We propose that positive feedback, common in biochemical pathways to switch between signaling states, can also be used in a mechanical signaling pathway to switch between structural states, in this case between short and long polymers. DOI: http://dx.doi.org/10.7554/eLife.10542.001

Regulation of a Spindle Positioning Factor at Kinetochores by SUMO-Targeted Ubiquitin Ligases

Correct function of the mitotic spindle requires balanced interplay of kinetochore and astral microtubules that mediate chromosome segregation and spindle positioning, respectively. Errors therein can cause severe defects ranging from aneuploidy to developmental disorders. Here, we describe a protein degradation pathway that functionally links astral microtubules to kinetochores via regulation of a microtubule-associated factor. We show that the yeast spindle positioning protein Kar9 localizes not only to astral but also to kinetochore microtubules, where it becomes targeted for proteasomal degradation by the SUMO-targeted ubiquitin ligases (STUbLs) Slx5-Slx8. Intriguingly, this process does not depend on preceding sumoylation of Kar9 but rather requires SUMO-dependent recruitment of STUbLs to kinetochores. Failure to degrade Kar9 leads to defects in both chromosome segregation and spindle positioning. We propose that kinetochores serve as platforms to recruit STUbLs in a SUMO-dependent manner in order to ensure correct spindle function by regulating levels of microtubule-associated proteins.

Arp1, an actin-related protein, in Plasmodium berghei.

Actin-related proteins (Arps) constitute a family of eukaryotic cytoskeletal proteins involved in such diverse events as cell motility, cytokinesis, vesicle transport, and chromatin remodelling. Previously, in a study of Plasmodium berghei gene expression in ookinetes and oocysts, we detected stage-specific increased expression of a gene encoding an Arp. Here we further characterize this gene and the encoded protein. We present a phylogenetic and three-dimensional modelling analysis as well as cell biological and genetic data that support classification of this gene as being an orthologue of the actin-related protein 1 (Arp1). This gene was found to be expressed in asexual stages as well as in the mosquito stages of the parasite, both on the transcript and protein level. Our attempts to delete the gene in the parasite for functional studies were unsuccessful, suggesting that it may be essential. The protein was localized apically of the nucleus in ookinetes, and in combination with the known function of Arp1 proteins, this suggests a role in vesicular transport. Expression of the gene in Saccharomyces cerevisiae resulted in toxic effects and interference with the yeast cytoskeleton.