Function and regulation of Cullin-RING ubiquitin ligases

Cullin–RING complexes comprise the largest known class of ubiquitin ligases. Owing to the great diversity of their substrate-receptor subunits, it is possible that there are hundreds of distinct cullin–RING ubiquitin ligases in eukaryotic cells, which establishes these enzymes as key mediators of post-translational protein regulation. In this review, we focus on the composition, regulation and function of cullin–RING ligases, and describe how these enzymes can be characterized by a set of general principles

Evidence of Secular Changes in Rainfall Data from the Tropical Western and Central Pacific over a 20-year Period

Rainfall data from the tropical western and central Pacific over the period from 1971 to 1990 show both decadal and interannual variability. A statistically significant secular trend may be used to model the overall rainfall variability. However, locally weighted regression analysis reveals that this increasing trend stalls in the early 1980\u27 s, and reverses its course by the year 1990. Decomposition of individual rainfall time series into low frequency, seasonal, and irregular components facilitates the isolation of the time varying annual cycle and the elucidation of the interannual signal. Strong or prolonged warm EI Nino-Southern Oscillation events dominate the interannual variability during the study period. The decadal scale variation in the annual cycle is so systematic, in fact, there is approximately a 20% reduction in its amplitude between 1971 and 1982. In addition, the long-term change in the seasonal component appears to modulate the much shorter-term interannual signal

The Acidic Tail of the Cdc34 Ubiquitin-conjugating Enzyme Functions in Both Binding to and Catalysis with Ubiquitin Ligase SCFC^(dc4*)

Ubiquitin ligases, together with their cognate ubiquitin-conjugating enzymes, are responsible for the ubiquitylation of proteins, a process that regulates a myriad of eukaryotic cellular functions. The first cullin-RING ligase discovered, yeast SCF^(Cdc4), functions with the conjugating enzyme Cdc34 to regulate the cell cycle. Cdc34 orthologs are notable for their highly acidic C-terminal extension. Here we confirm that the Cdc34 acidic C-terminal tail has a role in Cdc34 binding to SCF^(Cdc4) and makes a major contribution to the submicromolar K_m of Cdc34 for SCF^(Cdc4). Moreover, we demonstrate that a key functional property of the tail is its acidity. Our analysis also uncovers an unexpected new function for the acidic tail in promoting catalysis. We demonstrate that SCF is functional when Cdc34 is fused to the C terminus of Cul1 and that this fusion retains partial function even when the acidic tail has been deleted. The Cdc34-SCF fusion proteins that lack the acidic tail must interact in a fundamentally different manner than unfused SCF and wild type Cdc34, demonstrating that distinct mechanisms of E2 recruitment to E3, as is seen in nature, can sustain substrate ubiquitylation. Finally, a search of the yeast proteome uncovered scores of proteins containing highly acidic stretches of amino acids, hinting that electrostatic interactions may be a common mechanism for facilitating protein assembly

The cyclomodulin cycle inhibiting factor (CIF) alters cullin neddylation dynamics

The bacterial effector protein cycle inhibiting factor (CIF) converts glutamine 40 of NEDD8 to glutamate (Q40E), causing cytopathic effects and inhibiting cell proliferation. Although these have been attributed to blocking the functions of cullin-RING ubiquitin ligases, how CIF modulates NEDD8-dependent signaling is unclear. Here we use conditional NEDD8-dependent yeast to explore the effects of CIF on cullin neddylation. Although CIF causes cullin deneddylation and the generation of free NEDD8 Q40E, inhibiting the COP9 signalosome (CSN) allows Q40E to form only on NEDD8 attached to cullins. In the presence of the CSN, NEDD8 Q40E is removed from cullins more rapidly than NEDD8, leading to a decrease in steady-state cullin neddylation. As NEDD8 Q40E is competent for cullin conjugation in the absence of functional CSN and with overexpression of the NEDD8 ligase Dcn1, our data are consistent with NEDD8 deamidation causing enhanced deneddylation of cullins by the CSN. This leads to a dramatic change in the extent of activated cullin-RING ubiquitin ligases

Infrastructures of immobility: enabling international distance education students in Africa to <i>not</i> move

There is now a large literature discussing how mobilities are part of contemporary everyday power geometries and is a resource to which people have unequal access (Massey 1994; Sheller and Urry 2006). This body of work has, thus, valorised mobility as a desirable good. Why some people choose immobility and what has to be mobilised to enable this immobility has received much less attention. This paper draws on interviews with international distance education students in Namibia and Zimbabwe studying at the University of South Africa (UNISA) to explore the spatio-temporal underpinnings to why students choose to remain at home while studying abroad and how this is arranged. It outlines the infrastructures of reach that enable student immobility and how their incomplete nature means that students have to rely on extensive systems of mobilities of other people and objects to ensure that their study progresses without their own educational mobility. In doing so we move away from considering immobility as a result of limited access to mobility. Instead we set out a new research agenda on why and how the infrastructures of immobilities are important in mobility research

EMMIE and engineering: What works as evidence to improve decisions?

While written by a proponent of realism, this article argues in favour of a pragmatic approach to evaluation. It argues that multiple sources of evidence collected using diverse research methods can be useful in conducting informative evaluations of programmes, practices and policies. It argues in particular that methods, even if their assumptions appear incommensurable with one another, should be chosen to meet the evidence needs of decision-makers. These evidence needs are captured in the acronym, EMMIE, which refers to Effect size, Mechanism, Moderator (or context), Implementation and Economic impact. Finally the article questions evidence hierarchies that are inspired by clinical trials, and suggests instead that, notwithstanding the clear differences in the physical and social worlds, engineering may provide a superior model for evaluators to try to emulate. And engineering is, above all, a pragmatic field

Super-Bridges Suspended Over Carbon Nanotube Cables

In this paper the new concept of super-bridges, i.e. kilometre-long bridges suspended over carbon nanotube cables, is introduced. The analysis shows that the use of realistic (thus defective) carbon nanotube bundles as suspension cables can enlarge the current limit main span by a factor of 3.Comment: 17 pages, 6 figures, 2 table

Functional Diversity and Structural Disorder in the Human Ubiquitination Pathway

The ubiquitin-proteasome system plays a central role in cellular regulation and protein quality control (PQC). The system is built as a pyramid of increasing complexity, with two E1 (ubiquitin activating), few dozen E2 (ubiquitin conjugating) and several hundred E3 (ubiquitin ligase) enzymes. By collecting and analyzing E3 sequences from the KEGG BRITE database and literature, we assembled a coherent dataset of 563 human E3s and analyzed their various physical features. We found an increase in structural disorder of the system with multiple disorder predictors (IUPred - E1: 5.97%, E2: 17.74%, E3: 20.03%). E3s that can bind E2 and substrate simultaneously (single subunit E3, ssE3) have significantly higher disorder (22.98%) than E3s in which E2 binding (multi RING-finger, mRF, 0.62%), scaffolding (6.01%) and substrate binding (adaptor/substrate recognition subunits, 17.33%) functions are separated. In ssE3s, the disorder was localized in the substrate/adaptor binding domains, whereas the E2-binding RING/HECT-domains were structured. To demonstrate the involvement of disorder in E3 function, we applied normal modes and molecular dynamics analyses to show how a disordered and highly flexible linker in human CBL (an E3 that acts as a regulator of several tyrosine kinase-mediated signalling pathways) facilitates long-range conformational changes bringing substrate and E2-binding domains towards each other and thus assisting in ubiquitin transfer. E3s with multiple interaction partners (as evidenced by data in STRING) also possess elevated levels of disorder (hubs, 22.90% vs. non-hubs, 18.36%). Furthermore, a search in PDB uncovered 21 distinct human E3 interactions, in 7 of which the disordered region of E3s undergoes induced folding (or mutual induced folding) in the presence of the partner. In conclusion, our data highlights the primary role of structural disorder in the functions of E3 ligases that manifests itself in the substrate/adaptor binding functions as well as the mechanism of ubiquitin transfer by long-range conformational transitions. © 2013 Bhowmick et al

A Generic Platform for Cellular Screening Against Ubiquitin Ligases

Ubiquitin signalling regulates most aspects of cellular life, thus deregulation of ubiquitylation has been linked with a number of diseases. E3 ubiquitin ligases provide substrate selectivity in ubiquitylation cascades and are therefore considered to be attractive targets for developing therapeutic molecules. In contrast to established drug target classes, such as protein kinases, GPCRs, hormone receptors and ion channels, ubiquitin drug discovery is in its early stages. This is, in part, due to the complexity of the ubiquitylation pathways and the lack of robust quantitative technologies that allow high-throughput screening of inhibitors. Here we report the development of a Ubiquitin Ligase Profiling system, which is a novel and generic cellular technology designed to facilitate identification of selective inhibitors against RING type E3 ubiquitin ligases. Utilization of this system requires a single co-transfection of cells with assay vectors, thereby enabling readout of E3 ubiquitin ligase catalytic activity within the cellular environment. Therefore, our robust high-throughput screening platform offers novel opportunities for the development of inhibitors against this difficult-to-target E3 ligase enzyme class