Guilt by association: the arginine case revisited

If the genetic code arose in an RNA world, present codon assignments may reflect primordial RNA-amino acid affinities. Whether aptamers selected from random pools to bind free amino acids do so using the cognate codons at their binding sites has been controversial. Here we defend and extend our previous analysis of arginine binding sites, and propose a model for the maintenance of codon-amino acid interactions through the evolution of amino acids from ribozyme cofactors into the building blocks of proteins.     

Life at the edge: the nuclear envelope and human disease

A group of human diseases, known as 'laminopathies', are associated with defects in proteins of the nuclear envelope. Most laminopathy mutations have been mapped to the A-type lamin gene, which is expressed in most adult cell types. So, why should different mutations in a near-ubiquitously expressed gene be associated with various discrete tissue-restricted diseases? Attempts to resolve this paradox are uncovering new molecular interactions #151; both inside the nucleus and at its periphery -- which indicate that the nuclear envelope has functions that go beyond mere housekeeping.     

Calcium- and cell cycle-dependent association of annexin 11 with the nuclear envelope

Annexin 11 is a widely expressed calcium- and phospholipid-binding protein that resides in the nucleoplasm in many cultured cell lines. This is in contrast to its most extensively characterized in vitro ligand, the small calcium-binding protein S100A6 (calcyclin), which is concentrated in the nuclear envelope. Here we have examined the significance of the association of annexin 11 and S100A6 by asking whether circumstances exist in which the two proteins occupy the same subcellular localization. First, we show that in both A431 and vascular smooth muscle cells, elevation of intracellular Ca2+ leads to translocation of annexin 11 from the nucleus to the nuclear envelope where it co-localizes with S100A6. We also demonstrate, using fusions of annexin 11 with green fluorescent protein, that whereas the C-terminal core domain of annexin 11 is essential for Ca2+ sensitivity, the N-terminal domain is required for targeting to the nuclear envelope. Second, we show that annexin 11 relocalizes to the nuclear envelope as A431 cells transit from early to mid-prophase. In late prophase, at the time of nuclear envelope breakdown, annexin 11 and S100A6 become intensely localized with lamina-associated polypeptide 2 to folds in the nuclear envelope. From metaphase to telophase S100A6 is degraded, but in late telophase annexin 11 associates with the reforming nuclear envelope before resuming a nucleoplasmic location in interphase. These results show that co-localization of annexin 11 and S100A6 at the nuclear envelope may be regulated either by elevation of intracellular Ca2+ or by cell cycle progression and provide the first evidence that these proteins may associate in vivo.     

The epigenetics of nuclear envelope organization and disease

Mammalian chromosomes and some specific genes have non-random positions within the nucleus that are tissue-specific and heritable. Work in many organisms has shown that genes at the nuclear periphery tend to be inactive and altering their partitioning to the interior results in their activation. Proteins of the nuclear envelope can recruit chromatin with specific epigenetic marks and can also recruit silencing factors that add new epigenetic modifications to chromatin sequestered at the periphery. Together these findings indicate that the nuclear envelope is a significant epigenetic regulator. The importance of this function is emphasized by observations of aberrant distribution of peripheral heterochromatin in several human diseases linked to mutations in NE proteins. These debilitating inherited diseases range from muscular dystrophies to the premature aging progeroid syndromes and the heterochromatin changes are just one early clue for understanding the molecular details of how they work. The architecture of the nuclear envelope provides a unique environment for epigenetic regulation and as such a great deal of research will be required before we can ascertain the full range of its contributions to epigenetics.     

Guilt by association: What p120-catenin has to hide

Members of the p120-catenin family associate with cadherins and regulate their stability at the plasma membrane. How p120-catenin limits cadherin endocytosis has long remained a mystery. In this issue, Nanes et al. (2012. J. Cell Biol. doi:10.1083/jcb.201205029) identify a conserved acidic motif within cadherins that acts as a physical platform for p120-catenin binding. However, in the absence of p120-catenin, the motif acts as an endocytic signal. These results provide new insight into p120-catenin’s role as guardian of intercellular junction dynamics.Adhesion receptors of the classical cadherin family have a major role in establishing tissue organization and maintaining tissue homeostasis (Gumbiner, 1996). Classical cadherins are transmembrane glycoproteins that use their extracellular domains to establish calcium-dependent trans homophilic interactions with cadherins in neighboring cells. To enhance adhesive strength, cadherin ectodomains oligomerize through lateral (cis) interactions, whereas their cytoplasmic domains anchor to the actomyosin cytoskeleton. The cytoplasmic domain of cadherins is highly conserved and binds to proteins called catenins. p120-catenin (p120) associates with the transmembrane adjacent domain (juxtamembrane; JMD) of the cadherin cytoplasmic tail, whereas β-catenin interacts with the more distal portion of cadherin’s cytoplasmic domain. β-Catenin in turn, binds α-catenin, which, through multiple interactions, both indirect and direct, can associate with the actin cytoskeleton (Perez-Moreno and Fuchs, 2006).Cellular rearrangements are orchestrated by dynamic assembly/disassembly of cadherin complexes. The process is fueled by endocytosis of cadherin complexes (Le et al., 1999; de Beco et al., 2009). Endocytosis can be stimulated by proteins that associate with cadherin–catenin complexes, including proteases that shed the cadherin ectodomains, and the ubiquitin ligase Hakai (Fujita et al., 2002). Cadherin internalization can be regulated by different pathways depending on the cellular context, involving clathrin-dependent and clathrin-independent mechanisms. These endocytic processes must be carefully regulated, as an untimely destabilization of cadherin-mediated adhesion can lead to alterations in tissue architecture and growth, features of several diseases, including cancers (Mosesson et al., 2008).In the past decade, p120 catenins (p120, ARVCF, δ-catenin, and p0071) have emerged as critical regulators of cadherin-mediated adhesion (Reynolds, 2007). p120, the founding family member, is a component of cadherin complexes (Reynolds et al., 1994), and its association with the cadherin JMD is important for retaining cadherins at the membrane (Ireton et al., 2002). Moreover, p120 loss causes rapid internalization of cadherins, followed by proteasomal and/or lysosomal-mediated degradation (Davis et al., 2003; Xiao et al., 2003a,b, 2005; Miyashita and Ozawa, 2007).Although these studies expose p120 as a master regulator of cadherin levels at the membrane, exactly how p120 governs cadherin endocytosis rates has remained unclear. Based upon experiments in which endocytic machinery components (clathrin, dynamin, and AP2) have been impaired (Chiasson et al., 2009) or cadherin endocytic motifs have been mutated (Hong et al., 2010; Troyanovsky et al., 2007), researchers have posited that p120 binding to cadherins may in some way prevent junctional complex endocytosis. In this issue, Nanes et al. add new molecular insights into the mechanism. The authors show that the VE-cadherin JMD functions as a bimodal platform for either p120 binding or endocytic signaling. Moreover, they identify a key conserved amino acid residue within the JMD, which, when mutated, blocks endocytosis without the need for p120.Recently, the cocrystallization of p120 bound to E-cadherin’s JMD has yielded insights into the essential residues of this binding interface (Ishiyama et al., 2010). Previous studies had attributed the core function of p120-cadherin to its ability to bind and mask a dileucine endocytic motif present in the JMD (Miyashita and Ozawa, 2007; Hong et al., 2010). The crystal structure showed that interactions between p120 and the JMD domain might be sufficient to sterically prevent accessibility of the dileucine cadherin endocytic motif to endocytic adaptors such as the AP2-clathrin adaptor, thereby placing this motif at the crux of the bimodal switch controlling the mutually exclusive binding of either p120 or the endocytic machinery.The affinity of p120 and AP2 for the JMD dileucine motif is similar, pointing toward the existence of a balanced regulation of cadherin endocytic rates and cadherin retention at the membrane. However, evaluating this balance in cellular contexts has not been possible because of the inability to uncouple p120 binding to the JMD and endocytosis. Nanes et al. (2012) have now overcome this hurdle. They first used a simulated model of the p120–E-cadherin crystal structure, which highlighted a conserved p120-binding region that is present in the JMD of both VE- and E-cadherin. However, the VE-cadherin JMD lacked endocytic dileucine and tyrosine residues present in E-cadherin, which are involved in clathrin internalization and Hakai-dependent ubiquitination, respectively.Because both types of adherens junctions undergo dynamic endocytic-based remodeling, the authors astutely realized that they might be able to exploit VE- and E-cadherin differences to unearth novel endocytic signals within the sequence that might be conserved among cadherins. To this end, the author first used mutant VE-cadherin chimeric proteins, consisting of the cytoplasmic domain of VE-cadherin fused to the extracellular domain of the IL-2 receptor, and internalization assays. They discovered that the core p120-binding region on its own was endocytosed, in a fashion similar to the full VE-cadherin cytoplasmic tail. This occurred in a clathrin-dependent manner, as previously observed in Kowalzcyk’s laboratory (Chiasson et al., 2009). Point mutagenesis identified some mutants no longer able to bind p120, which is consistent with previous findings (Thoreson et al., 2000). But the authors made an interesting finding: mutations in a conserved acidic motif (DEE) within the p120-core binding region of the JMD displayed loss of p120 binding and also blocked cadherin internalization (Fig. 1). Moreover, DEE mutant VE-cadherins localized stably at the membrane even in the absence of p120, although with an increased diffusion within the membrane. This increase in mobility suggests a reduction in cadherin lateral clustering, a process modulated by the binding of p120 to the JMD (Yap et al., 1998). Interestingly, in crystal structures, the E-cadherin JMD binding to p120 induced oligomerization of the complex (Ishiyama et al., 2010).Open in a separate windowFigure 1.Model of VE-cadherin stabilization at the cell membrane. (A) VE-cadherin binds to p120 and β-catenin. p120 associates with the juxtamembrane (JMD) domain of the cadherin cytoplasmic tail, whereas β-catenin binds to the more distal portion (catenin binding domain, CBD). Cadherin internalization is triggered by p120 dissociation, exposing a conserved endocytic factor recognition motif (DEE; 646–648) within the JMD. (B) When this motif is mutated in VE-cadherin, adherens junctions are resistant to endocytosis independent of p120 binding.These new tools now allow uncoupling of p120 binding from cadherin endocytosis, which will be instrumental in unraveling new p120 cadherin roles in cell adhesion. The VE-cadherin mutant that fails to bind to p-120 still coimmunoprecipitates with β-catenin. These findings are intriguing, given that overexpression of p120 can rescue the otherwise poor adhesive properties of cadherins mutant for β-catenin binding (Ohkubo and Ozawa, 1999). In addition, interactions between p120 and α-catenin at adherens junctions seem to contribute in preventing cadherin endocytosis (Troyanovsky et al., 2011). Given these collective results, it will be interesting in the future to measure the binding affinities of endocytosis-uncoupled VE-cadherin mutants for its binding partners.Overall, these data provide strong evidence that the JMD landing pad provides the nuts and bolts of the decision of whether an adherens junction remains at the cell surface or whether it is internalized. But who makes the decision? Recent results from Gumbiner’s group provide a possible clue. They show that cadherin activation stimulates the dephosphorylation of specific Ser/Thr residues within the N-terminal domain of p120, and this in turn stabilizes intercellular adhesion (Petrova et al., 2012).The new tools developed by Kowalczyk’s group (Nanes et al., 2012) will pave the way for researchers to dig further into the mechanism. In the current study, the authors use their newfound tools to analyze the consequences to cell migration when p120-JMD binding is uncoupled from endocytosis. In scratched monolayers of endothelial cells, cell migration was decreased. Importantly, when they examined the VE-cadherin mutant in which p120 binding was blocked but cadherin internalization could proceed normally, cell migration was largely normal. These findings indicate that the migration defects seen in the cells expressing the E-cadherin mutant are rooted in inhibition of endocytosis, rather than lack of p120 recruitment to junctions. They further suggest that endocytic trafficking of cadherins is necessary to transiently destabilize cell–cell contacts that otherwise impede migration. This notion is particularly intriguing given that when E-cadherins are stabilized at intercellular junctions, they can sequester proteins that are required for integrin-based migration (Livshits et al., 2012). Kowalczyk’s findings (Nanes et al., 2012) now suggest a means by which dynamic changes in intercellular adhesion can be achieved to trigger such downstream events.Although less well characterized, there are other regulatory circuits that might also be affected by transiently liberating p120 from intercellular junctions. Thus, for example, p120 enhances cadherin stability through its ability to interact with afadin and Rap1, thereby bridging connections with nectin intercellular junctions (Hoshino et al., 2005). Other direct and indirect p120 associates that might affect cadherin internalization include the endocytic adaptor Numb (Sato et al., 2011) and the signaling enzyme γ-secretase (Kiss et al., 2008). Additionally, p120 can also regulate Rac1 activity, which influences cadherin endocytosis in a clathrin-independent way (Akhtar and Hotchin, 2001). Thus, removing p120 or devising additional mutations to uncouple these interactions may be needed to fully unravel all the mysteries underlying p120’s power in governing intercellular adhesion in tissue development and maintenance (Davis and Reynolds, 2006; Elia et al., 2006; Perez-Moreno et al., 2006; Smalley-Freed et al., 2010; Marciano et al., 2011; Stairs et al., 2011; Chacon-Heszele et al., 2012; Kurley et al., 2012). That said, by dissecting p120’s web at the crossroads between intercellular junction stabilization and endocytosis, Kowalczyk and coworkers (Nanes et al., 2012) now illustrate the power of their approach and provide new insights into how similar strategies might ultimately enable this molecular crossword puzzle to be solved.     

The nuclear lamins and the nuclear envelope

The cell nucleus is separated from the rest of the cell by the nuclear envelope. The nuclear envelope, nuclear envelope proteins and nuclear lamina organise the structure of the entire nucleus and the chromatin via a myriad of interactions. These interactions are dynamic, change with the change (progress) of the cell cycle, with cell differentiation and with changes in cell physiology.     

Dystonia and the nuclear envelope

Mutations in torsinA cause dominantly inherited early-onset torsion dystonia in humans. In this issue of Neuron, Goodchild et al. show that torsinA knockout and knockin mice have similar phenotypes, which suggests that the mutant torsinA allele causes disease because it has decreased function. The experiments also highlight the possible role of nuclear envelope dynamics in maintaining normal neuronal function.     

The conserved carboxy-terminal cysteine of nuclear lamins is essential for lamin association with the nuclear envelope

We have analyzed the interaction of soluble nuclear lamins with the nuclear envelope by microinjection of normal and mutated lamins into the cytoplasm of Xenopus laevis oocytes. Our results demonstrate that the conserved cysteine of the carboxy-terminal tetrapeptide Cys Ala/Ser Ile Met of lamins is essential for their association with the nuclear envelope. Removal of this sequence or replacement of the cysteine by serine resulted in Xenopus lamin L1 remaining in a soluble, non-envelope-associated state within the nucleus. Similar mutations of Xenopus lamin A resulted in only partial reduction of nuclear envelope association, indicating that lamin A contains additional signals that can partially compensate for the lack of the cysteine. Mammalian lamin C lacks this tetrapeptide and is not associated with the nuclear envelope in our experimental system. Cloning of the tetrapeptide Cys Ala Ile Met to the carboxy terminus of human lamin C resulted in lamin being found in a nuclear envelope-associated form in oocytes. Mutations at the amino terminus and in the alpha-helical region of lamin L1 revealed that the carboxy terminus mediates the association of lamins with the nuclear envelope; however, this alone is insufficient for maintenance of a stable association with the nuclear envelope.     

Towards defining the nuclear proteome

Background

The nucleus is a complex cellular organelle and accurately defining its protein content is essential before any systematic characterization can be considered.

Results

We report direct evidence for 2,568 mammalian proteins within the nuclear proteome: the nuclear subcellular localization of 1,529 proteins based on a high-throughput subcellular localization protocol of full-length proteins and an additional 1,039 proteins for which clear experimental evidence is documented in published literature. This is direct evidence that the nuclear proteome consists of at least 14% of the entire proteome. This dataset was used to evaluate computational approaches designed to identify additional nuclear proteins.

Conclusion

This represents direct experimental evidence that the nuclear proteome consists of at least 14% of the entire proteome. This high-quality nuclear proteome dataset was used to evaluate computational approaches designed to identify additional nuclear proteins. Based on this analysis, researchers can determine the stringency and types of lines of evidence they consider to infer the size and complement of the nuclear proteome.     

P446L-importin-beta inhibits nuclear envelope assembly by sequestering nuclear envelope assembly factors to the microtubules

The P446L mutant Drosophila importin-beta (P446L-imp-beta) has been reported to prohibit--in dominant negative fashion--nuclear envelope (NE) assembly. Along elucidating the mode of action of P446L-imp-beta we studied in vitro NE assembly on Sepharose beads. While Drosophila embryo extracts support NE assembly over Sepharose beads coated with Ran, NE assembly does not take place in extracts supplied with exogenous P446L-imp-beta. A NE also forms over importin-beta-coated beads. Surprisingly, when immobilized to Sepharose beads P446L-imp-beta as efficiently recruits NE vesicles as normal importin-beta. The discrepancy in behavior of cytoplasmic and bead-bound P446L-imp-beta appears to be related to icreased--as compared to normal importin-beta--microtubule (MT) binding ability of P446L-imp-beta. While wild-type importin-beta is able to bind MTs and the binding decreases upon RanGTP interaction, P446L-imp-beta cannot be removed from the MTs by RanGTP. P446L-imp-beta, like normal importin-beta, binds some types of the nucleoporins that have been known to be required for NE assembly at the end of mitosis. It appears that the inhibitory effect of P446L-imp-beta on NE assembly is caused by sequestering some of the nucleoporins required for NE assembly to the MTs.