Engineering a Ubiquitin Ligase Reveals Conformational Flexibility Required for Ubiquitin Transfer

Protein ubiquitination regulates numerous cellular functions in eukaryotes. The prevailing view about the role of RING or U-box ubiquitin ligases (E3) is to provide precise positioning between the attached substrate and the ubiquitin-conjugating enzyme (E2). However, the mechanism of ubiquitin transfer remains obscure. Using the carboxyl terminus of Hsc70-interacting protein as a model E3, we show herein that although U-box binding is required, it is not sufficient to trigger the transfer of ubiquitin onto target substrates. Furthermore, additional regions of the E3 protein that have no direct contact with E2 play critical roles in mediating ubiquitin transfer from E2 to attached substrates. By combining computational structure modeling and protein engineering approaches, we uncovered a conformational flexibility of E3 that is required for substrate ubiquitination. Using an engineered version of the carboxyl terminus of Hsc70-interacting protein ubiquitin ligase as a research tool, we demonstrate a striking flexibility of ubiquitin conjugation that does not affect substrate specificity. Our results not only reveal conformational changes of E3 during ubiquitin transfer but also provide a promising approach to custom-made E3 for targeted proteolysis.Protein modification by ubiquitin and ubiquitin-like proteins is a common mechanism through which numerous cellular pathways are regulated (1). The canonical cascade of ubiquitination involves the action of three enzymes, termed E1, E2, and E3, which activate and then conjugate ubiquitin to its substrates (2, 3). The E3 ligase catalyzes the final step in ubiquitin transfer in a substrate-specific manner. Despite advances in understanding the enzymatic cascade of ubiquitination, the mechanism of ubiquitin transfer to the substrate remains an outstanding issue (4). In particular, the role of E3 ubiquitin ligases and how they adapt to progressively modified substrates to maintain specific ubiquitin chain topology is still a mystery.The known E3s belong to three protein families: HECT, RING, and U-box. HECT domain enzymes form a covalent intermediate with ubiquitin before the final transfer of ubiquitin to substrates. In contrast, RING and U-box E3s have been suggested to function as adaptors that position the substrate in close proximity to the E2-ubiquitin thioester (E2-Ub) (5). It has become common “wisdom” that the substrate has to be precisely positioned to get ubiquitinated (6). The positioning hypothesis originally predicted that E3 substrates would have a specific ubiquitination site. However, the absence of “consensus” ubiquitination sites has become apparent in an increasing list of E3 substrates (7–9). In addition, the crystal structures of several ubiquitination machinery components have revealed a puzzling gap (∼50 Å) between the substrate binding sites and the E2 active sites (10, 11). This raises a fundamental question in ubiquitin transfer. How does the ubiquitin molecule shuttle from the E2 to substrates? Though several interesting models for ubiquitin transfer have been proposed, only limited explicit experimental evidence support these models (4).We used carboxyl terminus of Hsc70-interacting protein (CHIP)³ as a model E3 system to investigate the role of substrate positioning in its ubiquitination. CHIP is a protein quality control E3 that consists of an NH₂-terminal tetratricopeptide repeat (TPR) domain, a helical linker domain, and a COOH-terminal U-box domain (12, 13). The TPR domain of CHIP binds directly to EEVD motifs located at the COOH termini of Hsc/Hsp70 and Hsp90, whereas the U-box domains possess ubiquitin ligase activity. CHIP recruits E2 enzymes of the Ubc4/5 family to ubiquitinate misfolded proteins that occupy the chaperone substrate-binding sites, thus remodeling the chaperones from protein-refolding complexes to complexes that promote degradation (14). Using the chaperone as an adaptor, CHIP targets a variety of substrates for ubiquitination (15). In the absence of substrates, CHIP is also able to ubiquitinate the bound chaperones (16). Thus, there is apparent substrate diversity for CHIP-mediated ubiquitination. Insights into the mechanism of action of CHIP have been provided by an x-ray crystal structure which reveals a remarkable, highly asymmetric dimer (25). Here, we demonstrate the existence of intrinsic structural flexibility in the CHIP homodimer that is required for substrate polyubiquitination. The flexible orientation allows CHIP to accommodate substrates with different sizes and structures. Mutations that restrict the flexibility of CHIP markedly decrease substrate ubiquitination, whereas maintaining flexibility enables us to rebuild a functional ubiquitin ligase with altered substrate specificity. Our results provide evidence for the importance of structural flexibility in E3 ligases, which we propose is of general importance to orchestrate progressive ubiquitin conjugation on substrates.     

A new 2D-based method for myocardial velocity strain and strain rate quantification in a normal adult and paediatric population: assessment of reference values

Background

Cardiac time intervals have been described as a measure of cardiac performance, where prolongation, shortening and delay of the different time intervals have been evaluated as markers of cardiac dysfunction. A relatively recently developed method with improved ability to measure cardiac events is Tissue Doppler Imaging (TDI), allowing accurate measurement of myocardial movements.

Methods

We propose the state diagram of the heart as a new visualization tool for cardiac time intervals, presenting comparative, normalized data of systolic and diastolic performance, providing a more complete overview of cardiac function. This study aimed to test the feasibility of the state diagram method by presenting examples demonstrating its potential use in the clinical setting and by performing a clinical study, which included a comparison of the state diagram method with established echocardiography methods (E/E' ratio, LVEF and WMSI). The population in the clinical study consisted of seven patients with non ST-elevation myocardial infarction (NSTEMI) and seven control subjects, individually matched according to age and gender. The state diagram of the heart was generated from TDI curves from seven positions in the myocardium, visualizing the inter- and intraventricular function of the heart by displaying the cardiac phases.

Results

The clinical examples demonstrated that the state diagram allows for an intuitive visualization of pathological patterns as ischemia and dyssynchrony. Further, significant differences in percentage duration between the control group and the NSTEMI group were found in eight of the totally twenty phases (10 phases for each ventricle), e.g. in the transition phases (Pre-Ejection and Post-Ejection). These phases were significantly longer (> 2.18%) for the NSTEMI group than for the control group (p < 0.05). No significant differences between the groups were found for the established echocardiography methods.

Conclusion

The test results clearly indicate that the state diagram has potential to be an efficient tool for visualization of cardiac dysfunction and for detection of NSTEMI.     

Glycoprotein 60 diversity in C. hominis and C. parvum causing human cryptosporidiosis in NSW, Australia

Management and control of cryptosporidiosis in human requires knowledge of Cryptosporidium species contributing to human disease. Markers that are able to provide information below the species level have become important tools for source tracking. Using the hypervariable surface antigen, glycoprotein 60 (GP60), C. hominis (n = 37) and C. parvum (n = 32) isolates from cryptosporidiosis cases in New South Wales, Australia, were characterised. Extensive variation was observed within this locus and the isolates could be divided into 8 families and 24 different subtypes. The subtypes identified have global distributions and indicate that anthroponotic and zoonotic transmission routes contribute to sporadic human cryptosporidiosis in NSW.     

Systems analysis of iron metabolism: the network of iron pools and fluxes

Background  

Every cell of the mammalian organism needs iron as trace element in numerous oxido-reductive processes as well as for transport and storage of oxygen. The very versatility of ionic iron makes it a toxic entity which can catalyze the production of radicals that damage vital membranous and macromolecular assemblies in the cell. The mammalian organism maintains therefore a complex regulatory network of iron uptake, excretion and intra-body distribution. Intracellular regulation in different cell types is intertwined with a global hormonal signalling structure. Iron deficiency as well as excess of iron are frequent and serious human disorders. They can affect every cell, but also the organism as a whole.     

LINEAGES THAT CHEAT DEATH: SURVIVING THE SQUEEZE ON RANGE SIZE

Evolutionary lineages differ greatly in their net diversification rates, implying differences in rates of extinction and speciation. Lineages with a large average range size are commonly thought to have reduced extinction risk (although linking low extinction to high diversification has proved elusive). However, climate change cycles can dramatically reduce the geographic range size of even widespread species, and so most species may be periodically reduced to a few populations in small, isolated remnants of their range. This implies a high and synchronous extinction risk for the remaining populations, and so for the species as a whole. Species will only survive through these periods if their individual populations are “threat tolerant,” somehow able to persist in spite of the high extinction risk. Threat tolerance is conceptually different from classic extinction resistance, and could theoretically have a stronger relationship with diversification rates than classic resistance. I demonstrate that relationship using primates as a model. I also show that narrowly distributed species have higher threat tolerance than widespread ones, confirming that tolerance is an unusual form of resistance. Extinction resistance may therefore operate by different rules during periods of adverse global environmental change than in more benign periods.     

Capillary circular dichroism

Circular dichroism (CD) has become an increasingly important tool in the study of biological molecules as it enables structural information to be obtained nondestructively on solution-phase samples. However, sample requirements for CD are often seen as being too high with protein backbone measurements in standard cuvettes typically requiring ～100-300 μL of 0.1 mg/ml protein. To address this issue, we have designed a new form of CD sample holder, which reduces the sample requirements of the technique by two orders of magnitude, with a sample requirement of less than 3 μl. This sample saving has been achieved through the use of extruded quartz capillaries, the sample being held within the internal diameter of the quartz capillary through capillary action. The extruded quartz capillaries exhibit remarkably little birefringence, although still transmitting high energy UV circularly polarized light. The optics associated with capillaries were investigated. A configuration has been adopted with the light beam of the spectrophotometer being focused in front of the front face of the capillary using a biconvex lens and advantage being taken of the additional focusing effect of the capillary itself. The focusing is vital to the low wavelength performance of the cell, where we have acquired reliable data down to 180 nm using a Jasco J-815 spectrophotometer. The system performance was validated with Na[Co(EDDS)].H(2)O (EDDS = N,N-ethylenediaminedisuccinic acid), concanavalin A, lysozyme, and progesterone.     

NMR structural analysis of the soluble domain of ZiaA-ATPase and the basis of selective interactions with copper metallochaperone Atx1

A Cu(I) metallochaperone, Atx1, interacts with the amino-terminal domain of a Cu(I)-transporting ATPase, PacS_N, but not with a domain of related Zn-transporting ATPase, ZiaA_N in Synechocystis PCC 6803. This is thought to prevent ZiaA_N from acquiring Cu(I), which it binds more tightly than Zn. Solution structures of Atx1, PacS_N, and the heterodimer were previously described. Here we report solution structural studies of the ZiaA_N soluble domain. Apo-ZiaA_N has a typical ferredoxin-like fold followed by an atypical 34 residues of unstructured polypeptide containing a His₇ motif. ZiaA_N competes with the metallochromic indicator 4-(2-pyridylazo)resorcinol for 1 equiv of Zn, which can be displaced by thiol-modifying p-mercuriphenylsulfonic acid, establishing that a high-affinity site involves thiols of the CXXC motif within the ferredoxin-like fold. A single equivalent of Zn affects nuclear magnetic resonance signals arising from the CXXC motif as well as all seven His residues. The presence of NMR-line broadening in both sites implies that Zn₁-ZiaA_N undergoes exchange phenomena, consistent with CXXC-bound Zn coincidentally sampling various His ligands. These Zn-dependent dynamic changes could either aid metal transfer or alter intramolecular interactions. No formation of Atx1–Cu(I)–ZiaA_N heterodimers was observed, and in the presence of equimolar ZiaA_N and PacS_N, only Atx1–Cu(I)–PacS_N complexes were detected. Residues flanking the CXXC motif of PacS_N (R₁₃-ASS₂₀) differ in charge and bulk from those of ZiaA_N (D₁₈-KLK₂₅) and make contacts in the Atx1–Cu(I)–PacS_N complex. Crucially, swapping these residues flanking the CXXC motifs of ZiaA_N and PacS_N reciprocally swaps partner choice by Atx1. These few residues of the two ATPases have diverged during evolution to bias Atx1 interactions in favor of PacS_N rather than ZiaA_N.