Retromer-mediated recruitment of the WASH complex involves discrete interactions between VPS35, VPS29, and FAM21

Endosomal trafficking ensures the proper distribution of lipids and proteins to various cellular compartments, facilitating intracellular communication, nutrient transport, waste disposal, and the maintenance of cell structure. Retromer, a peripheral membrane protein complex, plays an important role in this process by recruiting the associated actin-polymerizing WASH complex to establish distinct sorting domains. The WASH complex is recruited through the interaction of the VPS35 subunit of retromer with the WASH complex subunit FAM21. Here, we report the identification of two separate fragments of FAM21 that interact with VPS35, along with a third fragment that binds to the VPS29 subunit of retromer. The crystal structure of VPS29 bound to a peptide derived from FAM21 shows a distinctive sharp bend that inserts into a conserved hydrophobic pocket with a binding mode similar to that adopted by other VPS29 effectors. Interestingly, despite the network of interactions between FAM21 and retromer occurring near the Parkinson's disease-linked mutation (D620N) in VPS35, this mutation does not significantly impair the direct association with FAM21 in vitro.

Sequence-independent activity of a predicted long disordered segment of the human papillomavirus type 16 L2 capsid protein during virus entry

The activity of proteins is thought to be invariably determined by their amino acid sequence or composition, but we show that a long segment of a viral protein can support infection independent of its sequence or composition. During virus entry, the papillomavirus L2 capsid protein protrudes through the endosome membrane into the cytoplasm to bind cellular factors such as retromer required for intracellular virus trafficking. Here, we show that an ~110 amino acid segment of L2 is predicted to be disordered and that large deletions in this segment abolish infectivity of HPV16 pseudoviruses by inhibiting cytoplasmic protrusion of L2, association with retromer, and proper virus trafficking. The activity of these mutants can be restored by insertion of protein segments with diverse sequences, compositions, and chemical properties, including scrambled amino acid sequences, a tandem array of a short sequence, and the intrinsically disordered region of an unrelated cellular protein. The infectivity of mutants with small in-frame deletions in this segment directly correlates with the size of the segment. These results indicate that the length of the disordered segment, not its sequence or composition, determines its activity during HPV16 pseudovirus infection. We propose that a minimal length of L2 is required for it to protrude far enough into the cytoplasm to bind cytoplasmic trafficking factors, but the sequence of this segment is largely irrelevant. Thus, protein segments can carry out complex biological functions such as Human papillomavirus pseudovirus infection in a sequence-independent manner. This finding has important implications for protein function and evolution.

Architecture of the ESCPE-1 membrane coat

Recycling of membrane proteins enables the reuse of receptors, ion channels and transporters. A key component of the recycling machinery is the endosomal sorting complex for promoting exit 1 (ESCPE-1), which rescues transmembrane proteins from the endolysosomal pathway for transport to the trans-Golgi network and the plasma membrane. This rescue entails the formation of recycling tubules through ESCPE-1 recruitment, cargo capture, coat assembly and membrane sculpting by mechanisms that remain largely unknown. Herein, we show that ESCPE-1 has a single-layer coat organization and suggest how synergistic interactions between ESCPE-1 protomers, phosphoinositides and cargo molecules result in a global arrangement of amphipathic helices to drive tubule formation. Our results thus define a key process of tubule-based endosomal sorting.

Wnt binding to Coatomer proteins directs secretion on exosomes independently of palmitoylation

Wnt proteins are secreted hydrophobic glycoproteins that act over long distances through poorly understood mechanisms. We discovered that Wnt7a is secreted on extracellular vesicles (EVs) following muscle injury. Structural analysis identified the motif responsible for Wnt7a secretion on EVs that we term the Exosome Binding Peptide (EBP). Addition of the EBP to an unrelated protein directed secretion on EVs. Disruption of palmitoylation, knockdown of WLS, or deletion of the N-terminal signal peptide did not affect Wnt7a secretion on purified EVs. Bio-ID analysis identified Coatomer proteins as candidates responsible for loading Wnt7a onto EVs. The crystal structure of EBP bound to the COPB2 coatomer subunit, the binding thermodynamics, and mutagenesis experiments, together demonstrate that a dilysine motif in the EBP mediates binding to COPB2. Other Wnts contain functionally analogous structural motifs. Mutation of the EBP results in a significant impairment in the ability of Wnt7a to stimulate regeneration, indicating that secretion of Wnt7a on exosomes is critical for normal regeneration in vivo . Our studies have defined the structural mechanism that mediates binding of Wnt7a to exosomes and elucidated the singularity of long-range Wnt signalling.

Sequence independent activity of a predicted long disordered segment of the human papillomavirus L2 capsid protein during virus entry

The papillomavirus L2 capsid protein protrudes through the endosome membrane into the cytoplasm during virus entry to bind cellular factors required for intracellular virus trafficking. Cytoplasmic protrusion of HPV16 L2, virus trafficking, and infectivity are inhibited by large deletions in an ∼110 amino acid segment of L2 that is predicted to be disordered. The activity of these mutants can be restored by inserting protein segments with diverse compositions and chemical properties into this region, including scrambled sequences, a tandem array of a short sequence, and the intrinsically disordered region of a cellular protein. The infectivity of mutants with small in-frame insertions and deletions in this segment directly correlates with the size of the segment. These results indicate that the length of the disordered segment, not its sequence or its composition, determines its activity during virus entry. Sequence independent but length dependent activity has important implications for protein function and evolution.

Structural insight into the membrane targeting domain of the Legionella deAMPylase SidD

AMPylation, the post-translational modification with adenosine monophosphate (AMP), is catalyzed by effector proteins from a variety of pathogens. Legionella pneumophila is thus far the only known pathogen that, in addition to encoding an AMPylase (SidM/DrrA), also encodes a deAMPylase, called SidD, that reverses SidM-mediated AMPylation of the vesicle transport GTPase Rab1. DeAMPylation is catalyzed by the N-terminal phosphatase-like domain of SidD. Here, we determined the crystal structure of full length SidD including the uncharacterized C-terminal domain (CTD). A flexible loop rich in aromatic residues within the CTD was required to target SidD to model membranes in vitro and to the Golgi apparatus within mammalian cells. Deletion of the loop (Δloop) or substitution of its aromatic phenylalanine residues rendered SidD cytosolic, showing that the hydrophobic loop is the primary membrane-targeting determinant of SidD. Notably, deletion of the two terminal alpha helices resulted in a CTD variant incapable of discriminating between membranes of different composition. Moreover, a L. pneumophila strain producing SidDΔloop phenocopied a L. pneumophila ΔsidD strain during growth in mouse macrophages and displayed prolonged co-localization of AMPylated Rab1 with LCVs, thus revealing that membrane targeting of SidD via its CTD is a critical prerequisite for its ability to catalyze Rab1 deAMPylation during L. pneumophila infection.

VPS29, a tweak tool of endosomal recycling

The endolysosomal system is a highly dynamic network of membranes for degradation and recycling. During endosomal maturation, cargo molecules destined for lysosomal degradation are progressively concentrated through continuous rounds of fusion and fission reactions concomitant with inbound and outbound membrane fluxes. Of the cargo molecules delivered to endosomes, about two-thirds are rescued from degradation and recycled for reuse. This balance between degradation and recycling is essential to preserve the proteostatic plasticity of the cell under variable physiological demands. Cargo retrieval from endosomes involves several sorting complexes with stable core compositions that associate with multidomain regulatory proteins, consequently displaying complex interaction networks. The vacuolar protein sorting 29 (VPS29) has emerged as a central scaffold that coordinates the physical assembly of retrieval complexes with regulatory components in what appears to be an elegant solution for regulating distinct retrieval stations. This review summarizes the VPS29-binding partners and its integration into retrieval complexes for endosomal sorting and trafficking.

Retromer

Lucas and Hierro introduce the retromer and its role in endosomal protein sorting and trafficking.

RavN is a member of a previously unrecognized group of Legionella pneumophila E3 ubiquitin ligases

The eukaryotic ubiquitylation machinery catalyzes the covalent attachment of the small protein modifier ubiquitin to cellular target proteins in order to alter their fate. Microbial pathogens exploit this post-translational modification process by encoding molecular mimics of E3 ubiquitin ligases, eukaryotic enzymes that catalyze the final step in the ubiquitylation cascade. Here, we show that the Legionella pneumophila effector protein RavN belongs to a growing class of bacterial proteins that mimic host cell E3 ligases to exploit the ubiquitylation pathway. The E3 ligase activity of RavN was located within its N-terminal region and was dependent upon interaction with a defined subset of E2 ubiquitin-conjugating enzymes. The crystal structure of the N-terminal region of RavN revealed a U-box-like motif that was only remotely similar to other U-box domains, indicating that RavN is an E3 ligase relic that has undergone significant evolutionary alteration. Substitution of residues within the predicted E2 binding interface rendered RavN inactive, indicating that, despite significant structural changes, the mode of E2 recognition has remained conserved. Using hidden Markov model-based secondary structure analyses, we identified and experimentally validated four additional L. pneumophila effectors that were not previously recognized to possess E3 ligase activity, including Lpg2452/SdcB, a new paralog of SidC. Our study provides strong evidence that L. pneumophila is dedicating a considerable fraction of its effector arsenal to the manipulation of the host ubiquitylation pathway.

Bacterial pathogens often hijack conserved host pathways by encoding proteins that are molecular mimics of eukaryotic enzymes, thus tricking the host cell into surrendering its resources to the bacteria. Here, we show that the intracellular pathogen Legionella pneumophila uses such a strategy to exploit ubiquitylation, a conserved post-translational modification that is mediated by E3 ubiquitin ligases. L. pneumophila encodes molecular mimics of host E3 ligases, including the effector protein RavN, thereby subverting the ubiquitylation pathway for its own benefit during infection. Using protein crystallography, we show that the fold of RavN has only residual resemblance to conventional eukaryotic E3s, yet its mode of interaction with E2 enzymes, host proteins that are important for the ubiquitin transfer reaction, has been preserved throughout evolution. Inspired by the discovery of RavN, we performed an in silico fold homology search and discovered several additional E3 ligase candidates within the effector repertoire of L. pneumophila that, until now, had remained hidden due to lack of primary sequence similarity. Our study supports the hypothesis that E3 ligases are a vital part of the virulence program of L. pneumophila, and that these effectors, despite having undergone extensive evolutionary changes, have retained features that are critical for their biological function, including the ability to hijack host factors that are part of the ubiquitylation machinery.

Quantitative analysis of the interplay between InAs quantum dots and wetting layer during the GaAs capping process

A procedure to quantitatively analyse the relationship between the wetting layer (WL) and the quantum dots (QDs) as a whole in a statistical way is proposed. As we will show in the manuscript, it allows determining, not only the proportion of deposited InAs held in the WL, but also the average In content inside the QDs. First, the amount of InAs deposited is measured for calibration in three different WL structures without QDs by two methodologies: strain mappings in high-resolution transmission electron microscopy images and compositional mappings with ChemiSTEM x-ray energy spectrometry. The area under the average profiles obtained by both methodologies emerges as the best parameter to quantify the amount of InAs in the WL, in agreement with high-resolution x-ray diffraction results. Second, the effect of three different GaAs capping layer (CL) growth rates on the decomposition of the QDs is evaluated. The CL growth rate has a strong influence on the QD volume as well as the WL characteristics. Slower CL growth rates produce an In enrichment of the WL if compared to faster ones, together with a diminution of the QD height. In addition, assuming that the QD density does not change with the different CL growth rates, an estimation of the average In content inside the QDs is given. The high Ga/In intermixing during the decomposition of buried QDs does not only trigger a reduction of the QD height, but above all, a higher impoverishment of the In content inside the QDs, therefore modifying the two most important parameters that determine the optical properties of these structures.

Dose assessment to workers in a dicalcium phosphate production plant

The production of dicalcium phosphate (DCP) uses phosphate rock (PR) as a raw material. Sedimentary phosphate rocks are enriched with relevant concentrations of natural radionuclides from the ²³⁸U decay chain (around 10³ Bq·kg^-1), leading to the need of controlling potential exposures to radiation of workers and members of the public in accordance with IAEA safety standards. Indeed, phosphate industries are classified as Naturally Occurring Radioactive Material (NORM) industries. Thus, the aim of this work is to assess the radiological risk of the workers in a DCP production plant located in the Iberian Peninsula (South-West Europe), which digests PR with hydrochloric acid. In the present study ²³⁸U, ²³⁰Th, ²²²Rn, ²¹⁰Pb and ²¹⁰Po concentrations in aerosols (indoor and outdoor areas) are reported. Aerosols showed concentrations between 0.42-92 mBq·m^-3 for ²³⁸U, 0.24-33 mBq·m^-3 for ²³⁰Th, 0.67-147 mBq·m^-3 for ²¹⁰Pb and 0.09-34 mBq·m^-3 for ²¹⁰Po. Long-term exposure (four months) of passive ²²²Rn detectors provided concentrations that ranged from detection limit (< DL) to 121 Bq·m^-3 in outdoor areas and from < DL to 211 Bq·m^-3 in indoor areas, similar to concentrations obtained from short-term measurements with active detectors from < DL to 117 Bq·m^-3 in outdoor areas and from < DL to 318 Bq·m^-3 in indoor places. ²²⁶Ra accumulation in ebonite and pipe scales were the most important contributions to the ambient dose equivalent H*(10), resulting in 0.07 (background)-27 μSv·h^-1 with a median value of 1.1 μSv·h^-1. Average ²²²Rn air concentrations were lower than the 300 Bq·m^-3 limit and therefore, according to European Directive 2013/59/EURATOM, ²²²Rn concentration is excluded from the worker operational annual effective dose. Thus, considering the inhalation of aerosols and the external dose sources, the total effective dose determined for plant operators was 0.37 mSv·y^-1.

Structural Mechanism for Cargo Recognition by the Retromer Complex

Retromer is a multi-protein complex that recycles transmembrane cargo from endosomes to the trans-Golgi network and the plasma membrane. Defects in retromer impair various cellular processes and underlie some forms of Alzheimer's disease and Parkinson's disease. Although retromer was discovered over 15 years ago, the mechanisms for cargo recognition and recruitment to endosomes have remained elusive. Here, we present an X-ray crystallographic analysis of a four-component complex comprising the VPS26 and VPS35 subunits of retromer, the sorting nexin SNX3, and a recycling signal from the divalent cation transporter DMT1-II. This analysis identifies a binding site for canonical recycling signals at the interface between VPS26 and SNX3. In addition, the structure highlights a network of cooperative interactions among the VPS subunits, SNX3, and cargo that couple signal-recognition to membrane recruitment.

General route for the decomposition of InAs quantum dots during the capping process

The effect of the capping process on the morphology of InAs/GaAs quantum dots (QDs) by using different GaAs-based capping layers (CLs), ranging from strain reduction layers to strain compensating layers, has been studied by transmission microscopic techniques. For this, we have measured simultaneously the height and diameter in buried and uncapped QDs covering populations of hundreds of QDs that are statistically reliable. First, the uncapped QD population evolves in all cases from a pyramidal shape into a more homogenous distribution of buried QDs with a spherical-dome shape, despite the different mechanisms implicated in the QD capping. Second, the shape of the buried QDs depends only on the final QD size, where the radius of curvature is function of the base diameter independently of the CL composition and growth conditions. An asymmetric evolution of the QDs' morphology takes place, in which the QD height and base diameter are modified in the amount required to adopt a similar stable shape characterized by a averaged aspect ratio of 0.21. Our results contradict the traditional model of QD material redistribution from the apex to the base and point to a different universal behavior of the overgrowth processes in self-organized InAs QDs.

Formation of Tubulovesicular Carriers from Endosomes and Their Fusion to the trans-Golgi Network

Endosomes undergo extensive spatiotemporal rearrangements as proteins and lipids flux through them in a series of fusion and fission events. These controlled changes enable the concentration of cargo for eventual degradation while ensuring the proper recycling of other components. A growing body of studies has now defined multiple recycling pathways from endosomes to the trans-Golgi network (TGN) which differ in their molecular machineries. The recycling process requires specific sets of lipids, coats, adaptors, and accessory proteins that coordinate cargo selection with membrane deformation and its association with the cytoskeleton. Specific tethering factors and SNARE (SNAP (Soluble NSF Attachment Protein) Receptor) complexes are then required for the docking and fusion with the acceptor membrane. Herein, we summarize some of the current knowledge of the machineries that govern the retrograde transport from endosomes to the TGN.

Role of cholesterol in SNARE-mediated trafficking on intracellular membranes

The cell surface delivery of extracellular matrix (ECM) and integrins is fundamental for cell migration in wound healing and during cancer cell metastasis. This process is not only driven by several soluble NSF attachment protein (SNAP) receptor (SNARE) proteins, which are key players in vesicle transport at the cell surface and intracellular compartments, but is also tightly modulated by cholesterol. Cholesterol-sensitive SNAREs at the cell surface are relatively well characterized, but it is less well understood how altered cholesterol levels in intracellular compartments impact on SNARE localization and function. Recent insights from structural biology, protein chemistry and cell microscopy have suggested that a subset of the SNAREs engaged in exocytic and retrograde pathways dynamically 'sense' cholesterol levels in the Golgi and endosomal membranes. Hence, the transport routes that modulate cellular cholesterol distribution appear to trigger not only a change in the location and functioning of SNAREs at the cell surface but also in endomembranes. In this Commentary, we will discuss how disrupted cholesterol transport through the Golgi and endosomal compartments ultimately controls SNARE-mediated delivery of ECM and integrins to the cell surface and, consequently, cell migration.

Mobility of Po and U-isotopes under acid mine drainage conditions: an experimental approach with samples from Río Tinto area (SW Spain)

Under acid mine drainage (AMD) conditions, the solubilities and mobilities of many elements are vastly different from conditions prevailing in most natural waters. Studies are underway in the Río Tinto area (Iberian Pyrite Belt), in order to understand the behavior and mobility of long-lived U-series radionuclides under AMD conditions. A set of leaching experiments utilizing typical country rocks from the Tinto River basin, waste rock pile composite materials, iron-rich riverbed sediments and gossan (weathered naturally rock) were performed towards this purpose. Initial leaching experiments using distilled water kept in contact with solid material for 300, 100, 50 and 1 h resulted in very low concentrations of U with (234)U/(238)U activity ratios close to equilibrium and activity concentrations of (210)Po < 0.03 mBq/g. Leaching experiments performed with sulfuric acid media (0.1 and 0.01 M), and contact times between the solid and solution for 24 h were conducted to quantify the amount of U-isotopes and (210)Po leached, and the radioactive disequilibria generated between the radionuclides in the leachate. These experiments show that Po mobility in acidic conditions (pH around 1-2) is very low, with (210)Po activity in the leachate to be 6% in average for the solid sample. By contrast, mobility of U-isotopes is higher than that of Po, around 1.2%.

Trace metal partitioning over a tidal cycle in an estuary affected by acid mine drainage (Tinto estuary, SW Spain)

The Tinto River estuary is highly polluted with the acid lixiviates from old sulphide mines. In this work the behaviour of dissolved and particulate trace metals under strong chemical gradients during a tidal cycle is studied. The pH values range from 4.4 with low tide to 6.9 with high tide. Precipitation of Fe and Al is intense during rising tides and As and Pb are almost exclusively found in the particulate matter (PM). Sorption processes are very important in controlling the mobility (and hence bioavailability) of some metals and particularly affect Cu below pH 6. Above pH~6 Cu is desorbed, probably by the formation of Cu(I)-chloride complexes. Although less pronounced than Cu, also Zn desorption above pH 6.5 seems to occur. Mn and Co are affected by sorption processes at pH higher than ca. 6. Cd behaves conservatively and Ni is slightly affected by sorption processes.

Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5

A challenge for microbial pathogens is to assure that their translocated effector proteins target only the correct host cell compartment during infection. The Legionella pneumophila effector vacuolar protein sorting inhibitor protein D (VipD) localizes to early endosomal membranes and alters their lipid and protein composition, thereby protecting the pathogen from endosomal fusion. This process requires the phospholipase A1 (PLA1) activity of VipD that is triggered specifically on VipD binding to the host cell GTPase Rab5, a key regulator of endosomes. Here, we present the crystal structure of VipD in complex with constitutively active Rab5 and reveal the molecular mechanism underlying PLA1 activation. An active site-obstructing loop that originates from the C-terminal domain of VipD is repositioned on Rab5 binding, thereby exposing the catalytic pocket within the N-terminal PLA1 domain. Substitution of amino acid residues located within the VipD-Rab5 interface prevented Rab5 binding and PLA1 activation and caused a failure of VipD mutant proteins to target to Rab5-enriched endosomal structures within cells. Experimental and computational analyses confirmed an extended VipD-binding interface on Rab5, explaining why this L. pneumophila effector can compete with cellular ligands for Rab5 binding. Together, our data explain how the catalytic activity of a microbial effector can be precisely linked to its subcellular localization.

VIS-UV ZnCdO/ZnO multiple quantum well nanowires and the quantification of Cd diffusion

We report on the growth and microstructure analysis of high Cd content ZnCdO/ZnO multiple quantum wells (MQW) within a nanowire. Heterostructures consisting of ten wells with widths from 0.7 to 10 nm are demonstrated, and show photoluminescence emissions ranging from 3.03 to 1.97 eV. The wells with thicknesses ≦̸2 nm have high radiative efficiencies compared to the thickest ones, consistent with the presence of quantum confinement. However, a nanometric analysis of the Cd profile along the heterostructures shows the presence of Cd diffusion from the ZnCdO well to the ZnO barrier. This phenomenon modifies the band structure and the optical properties of the heterostructure, and is considered in order to correctly identify quantum effects in the ZnCdO/ZnO MQWs.

Geochemical behavior of metals and metalloids in an estuary affected by acid mine drainage (AMD)

The Tinto and Odiel rivers in southwest Spain drain the world's largest sulfide mineral formation: the Iberian Pyrite Belt which has been worked since 2,500 BC. The Tinto and Odiel estuarine zones include both an extensive area of salt marsh and an intensively industrialized urban area. As a consequence of pyrite oxidation, the Tinto and Odiel rivers are strongly acidic (pH < 3) with unusually high and quite variable metal concentrations. In this study, seasonally varying concentrations of dissolved major and trace elements were determined in the acid mine drainage affected estuary of the Ría de Huelva. During estuarine mixing, ore-derived metal concentrations exhibit excellent correlations with pH as the main controlling parameter. As pH increases, concentrations of dissolved ore-associated elements are attenuated, and this process is enhanced during the summer months. The decrease in Fe and Al concentrations ranged from 80 to 100 % as these elements are converted from dissolved to sediment-associated forms in the estuary. Coprecipitation/adsorption processes also removed between 60 and 90 % of the originally dissolved Co, Cu, Mn, Pb, Zn, and Th; however, Cd and Ni exhibited a greater propensity to remain in solution, with an average removal of approximately 60 %. On the other hand, As and U exhibited a different behavior; it is likely that these elements remain in dissolved forms because of the formation of U carbonates and soluble As species. Concentrations of As remain at elevated levels in the outer estuary (average = 48 μg L(-1)) which exceeds concentrations present in the Tinto River. Nevertheless, the estuary has recently witnessed improvements in water quality, as compared to results of several previous studies reported in the 1990s.

Large negative thermal expansion of the Co subnetwork measured by EXAFS in highly disordered Nd₁-xCox thin films with perpendicular magnetic anisotropy

We have measured a negative thermal expansion (NTE) of the Co subnetwork in amorphous Nd1-xCox (0.78 < x < 0.84) thin films of the order of 1% in volume using linearly polarized EXAFS spectroscopy at RT and 10 K. The expansion, which is anisotropic, is uncorrelated with the perpendicular magnetic anisotropy (PMA) observed in all the films, but correlated with the method used to deposit them. The atomic environments of the Nd atoms resulted in such a strong disorder that Nd-Nd and Nd-Co environments were invisible to EXAFS, and only Co-Co atomic environments were detected. The information on the Nd subnetwork was obtained through its magnetic moment measured by XMCD. These measurements demonstrate an increasing interaction of neodymium atoms with their particular local crystal field as the temperature decreased, suggesting possible structural modifications at their sites. Since the magnetic moment of the cobalt subnetwork remains essentially constant with the temperature, it is proposed that its detected NTE may be caused by the mechanical response of the amorphous network to structural transformations at the Nd sites. These results support that the PMA in RE-TM alloys is localized at the RE sites. The complete absence of EXAFS oscillations in the Nd L3 EXAFS spectra is remarkable: it means that the coherence length of the photoemitted electrons in disordered matter can be strongly reduced from that expected by atomic calculations to the point of being less than first neighbor distances, which is contrary to the common belief that first neighbors are always visible by EXAFS.

Uranium behaviour in an estuary polluted by mining and industrial effluents: the Ría of Huelva (SW of Spain)

This paper describes a comprehensive study of the behaviour of U in the Ría of Huelva estuary, formed by the Tinto and Odiel rivers. This ecosystem is conditioned by two hydrochemical facts: one connected with the acid mining drainage (AMD) generated in the first section of the river basins, and another one related to the fertilizer industry located at the estuary. AMD gives a singular character to these rivers; low pH and high redox potential that keep high amounts of toxic elements and radionuclides in dissolution. Most of the data for dissolved U in estuaries indicate conservative mixing, but there are examples of non-conservative behaviour attributed to oxidation/reduction processes or solubility variations. In the Ría of Huelva estuary the U shows a non-conservative behaviour due to solubility changes produced by variations in the pH. A complete removal of riverine dissolved U is observed in a pH range of 4-6. At higher pH values, U release from suspended matter, and probably also from sediments into the dissolved phase is found.

Structural basis for the interaction of the Golgi-Associated Retrograde Protein Complex with the t-SNARE Syntaxin 6

The Golgi-Associated Retrograde Protein (GARP) complex is a tethering factor involved in the fusion of endosome-derived transport vesicles to the trans-Golgi network through interaction with components of the Syntaxin 6/Syntaxin 16/Vti1a/VAMP4 SNARE complex. The mechanisms by which GARP and other tethering factors engage the SNARE fusion machinery are poorly understood. Herein, we report the structural basis for the interaction of the human Ang2 subunit of GARP with the Syntaxin 6 and the closely related Syntaxin 10. The crystal structure of the Syntaxin 6 Habc domain in complex with a peptide from the N terminus of Ang2 shows a binding mode in which a dityrosine motif of Ang2 interacts with a highly conserved groove in Syntaxin 6. Structure-based mutational analyses validate the crystal structure and support the phylogenetic conservation of this interaction.

Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD

The covalent attachment of adenosine monophosphate (AMP) to proteins, a process called AMPylation (adenylylation), has recently emerged as a novel theme in microbial pathogenesis. Although several AMPylating enzymes have been characterized, the only known virulence protein with de-AMPylation activity is SidD from the human pathogen Legionella pneumophila. SidD de-AMPylates mammalian Rab1, a small GTPase involved in secretory vesicle transport, thereby targeting the host protein for inactivation. The molecular mechanisms underlying Rab1 recognition and de-AMPylation by SidD are unclear. Here, we report the crystal structure of the catalytic region of SidD at 1.6 Å resolution. The structure reveals a phosphatase-like fold with additional structural elements not present in generic PP2C-type phosphatases. The catalytic pocket contains a binuclear metal-binding site characteristic of hydrolytic metalloenzymes, with strong dependency on magnesium ions. Subsequent docking and molecular dynamics simulations between SidD and Rab1 revealed the interface contacts and the energetic contribution of key residues to the interaction. In conjunction with an extensive structure-based mutational analysis, we provide in vivo and in vitro evidence for a remarkable adaptation of SidD to its host cell target Rab1 which explains how this effector confers specificity to the reaction it catalyses.

Behavior of natural radionuclides in surficial sediments from an estuary impacted by acid mine discharge and industrial effluents in Southwest Spain

The environmental degradation resulting from the acid mine drainage (AMD) and discharge from effluents of phosphogypsum (PG) piles in the watershed of Tinto and Odiel Rivers estuary over long periods of time has resulted in significant impact on the ecosystem of this estuary, resulting that the sediments are highly polluted by heavy metals and radionuclides from the discharge AMD and leachates from the PG. During resuspension of benthic sediments some of the radionuclides are desorbed making them bioavailable. In the present study, we investigate the spatial distribution of radionuclides U, Th and Ra and assess the factors and processes that caused the spatial distribution of these nuclides in this estuarine system. This study has global significance for other polluted environmental systems that are impacted by AMD and PG.

Metamorphic In(0.20)Ga(0.80)As p-i-n photodetectors grown on GaAs substrates for near infrared applications

The growth and performance of top-illuminated metamorphic In(0.20)Ga(0.80)As p-i-n photodetectors grown on GaAs substrates using a step-graded In(x)Ga(1-x)As buffer is reported. The p-i-n photodetectors display a low room-temperature reverse bias dark current density of ~1.4×10(-7) A/cm(2) at -2 V. Responsivity and specific detectivity values of 0.72 A/W, 2.3×10(12) cm·Hz(1/2)/W and 0.69 A/W, 2.2×10(12) cm·Hz(1/2)/W are achieved for Yb:YAG (1030 nm) and Nd:YAG (1064 nm) laser wavelengths at -2 V, respectively. A high theoretical bandwidth-responsivity product of 0.21 GHz·A/W was estimated at 1064 nm. Device performance metrics for these GaAs substrate-based detectors compare favorably with those based on InP technology due to the close tuning of the detector bandgap to the target wavelengths, despite the presence of a residual threading dislocation density. This work demonstrates the great potential for high performance metamorphic near-infrared InGaAs detectors with optimally tuned bandgaps, which can be grown on GaAs substrates, for a wide variety of applications.

Functional architecture of the retromer cargo-recognition complex

The retromer complex is required for the sorting of acid hydrolases to lysosomes, transcytosis of the polymeric immunoglobulin receptor, Wnt gradient formation, iron transporter recycling and processing of the amyloid precursor protein. Human retromer consists of two smaller complexes: the cargo recognition VPS26-VPS29-VPS35 heterotrimer and a membrane-targeting heterodimer or homodimer of SNX1 and/or SNX2 (ref. 13). Here we report the crystal structure of a VPS29-VPS35 subcomplex showing how the metallophosphoesterase-fold subunit VPS29 (refs 14, 15) acts as a scaffold for the carboxy-terminal half of VPS35. VPS35 forms a horseshoe-shaped, right-handed, alpha-helical solenoid, the concave face of which completely covers the metal-binding site of VPS29, whereas the convex face exposes a series of hydrophobic interhelical grooves. Electron microscopy shows that the intact VPS26-VPS29-VPS35 complex is a stick-shaped, flexible structure, approximately 21 nm long. A hybrid structural model derived from crystal structures, electron microscopy, interaction studies and bioinformatics shows that the alpha-solenoid fold extends the full length of VPS35, and that VPS26 is bound at the opposite end from VPS29. This extended structure presents multiple binding sites for the SNX complex and receptor cargo, and appears capable of flexing to conform to curved vesicular membranes.

Structural and functional organization of the ESCRT-I trafficking complex

The endosomal sorting complex required for transport (ESCRT) complexes are central to receptor downregulation, lysosome biogenesis, and budding of HIV. The yeast ESCRT-I complex contains the Vps23, Vps28, and Vps37 proteins, and its assembly is directed by the C-terminal steadiness box of Vps23, the N-terminal half of Vps28, and the C-terminal half of Vps37. The crystal structures of a Vps23:Vps28 core subcomplex and the Vps23:Vps28:Vps37 core were solved at 2.1 and 2.8 A resolution. Each subunit contains a structurally similar pair of helices that form the core. The N-terminal domain of Vps28 has a hydrophobic binding site on its surface that is conformationally dynamic. The C-terminal domain of Vps28 binds the ESCRT-II complex. The structure shows how ESCRT-I is assembled by a compact core from which the Vps23 UEV domain, the Vps28 C domain, and other domains project to bind their partners.

Polycistronic expression and purification of the ESCRT-II endosomal trafficking complex

Eukaryotic cells use sophisticated mechanisms to direct protein traffic between subcellular compartments. In eukaryotic cells, transmembrane proteins are delivered for degradation in the lysosome or yeast vacuole via multivesicular bodies. The sorting of proteins into lumenal vesicles within multivesicular bodies is directed by the three ESCRT protein complexes. Here we describe the expression and purification of the ESCRT-II complex using the polycistronic expression vector pST39 developed by Tan. In a modification of Tan's procedure, Pfu polymerase amplification with overlapping oligonucleotides was used to generate the translation cassettes for subcloning into pST39 expression vector in a single step. This approach reduces the number of restriction sites and subcloning steps required to express a heterooligomeric protein complex, facilitating rapid screening of multiple complexes and complex variants for crystallization or biochemical characterization.

Structural basis for endosomal targeting by the Bro1 domain

Proteins delivered to the lysosome or the yeast vacuole via late endosomes are sorted by the ESCRT complexes and by associated proteins, including Alix and its yeast homolog Bro1. Alix, Bro1, and several other late endosomal proteins share a conserved 160 residue Bro1 domain whose boundaries, structure, and function have not been characterized. The crystal structure of the Bro1 domain of Bro1 reveals a folded core of 367 residues. The extended Bro1 domain is necessary and sufficient for binding to the ESCRT-III subunit Snf7 and for the recruitment of Bro1 to late endosomes. The structure resembles a boomerang with its concave face filled in and contains a triple tetratricopeptide repeat domain as a substructure. Snf7 binds to a conserved hydrophobic patch on Bro1 that is required for protein complex formation and for the protein-sorting function of Bro1. These results define a conserved mechanism whereby Bro1 domain-containing proteins are targeted to endosomes by Snf7 and its orthologs.

Structure of the ESCRT-II endosomal trafficking complex

The multivesicular-body (MVB) pathway delivers transmembrane proteins and lipids to the lumen of the endosome. The multivesicular-body sorting pathway has crucial roles in growth-factor-receptor downregulation, developmental signalling, regulation of the immune response and the budding of certain enveloped viruses such as human immunodeficiency virus. Ubiquitination is a signal for sorting into the MVB pathway, which also requires the functions of three protein complexes, termed ESCRT-I, -II and -III (endosomal sorting complex required for transport). Here we report the crystal structure of the core of the yeast ESCRT-II complex, which contains one molecule of the Vps protein Vps22, the carboxy-terminal domain of Vps36 and two molecules of Vps25, and has the shape of a capital letter 'Y'. The amino-terminal coiled coil of Vps22 and the flexible linker leading to the ubiquitin-binding NZF domain of Vps36 both protrude from the tip of one branch of the 'Y'. Vps22 and Vps36 form nearly equivalent interactions with the two Vps25 molecules at the centre of the 'Y'. The structure suggests how ubiquitinated cargo could be passed between ESCRT components of the MVB pathway through the sequential transfer of ubiquitinated cargo from one complex to the next.

Activation mechanism of the nuclear chaperone nucleoplasmin: role of the core domain

Nucleoplasmin (NP) mediates nucleosome assembly by removing basic proteins from sperm chromatin and exchanging them with histones. This function is modulated by phosphorylation of NP at multiple sites. NP is pentameric, each monomer consisting of two domains: a core, which forms a stable ring-like pentamer, and a tail, that holds a polyglutamic tract and the nuclear localization signal. In the present study, we have explored the role of the core domain in the functionality of NP. Despite lacking the poly-Glu region, a putative binding site for basic proteins, the isolated core domain of the hyperphosphorylated protein isolated from eggs of Xenopus laevis is able to bind sperm basic proteins and decondense chromatin, in contrast to the inactive, non-phosphorylated recombinant core. This activity can be reproduced artificially in the recombinant core domain through mutation of putative phosphorylation sites to aspartate, thus mimicking the charge effect of phosphorylation. The mutated residues locate in flexible or loop regions exposed on the "distal face" of the core pentamer, where a short acidic region is also found, indicating that phosphorylation might activate the core domain of NP by generating a strong localized negative potential. Our results show that the phosphorylated core domain of NP is active in chromatin decondensation, thus it could contribute together with the poly-Glu containing tail in displaying a binding surface for sperm basic proteins on the NP pentamer.

Electrostatic interactions at the C-terminal domain of nucleoplasmin modulate its chromatin decondensation activity

The chromatin decondensation activity, thermal stability, and secondary structure of recombinant nucleoplasmin, of two deletion mutants, and of the protein isolated from Xenopus oocytes have been characterized. As previously reported, the chromatin decondensation activity of recombinant, unphosphorylated nucleoplasmin is almost negligible. Our data show that deletion of 50 residues at the C-terminal domain of the protein, containing the positively charged nuclear localization sequence, activates its chromatin decondensation ability and decreases its stability. Interestingly, both the decondensation activity and thermal stability of this deletion mutant resemble those of the phosphorylated protein isolated from Xenopus oocytes. Deletion of 80 residues at the C-terminal domain, containing the above-mentioned positively charged region and a poly(Glu) tract, inactivates the protein and increases its thermal stability. These findings, along with the effect of salt on the thermal stability of these proteins, suggest that electrostatic interactions between the positive nuclear localization sequence and the poly(Glu) tract, at the C-terminal domain, modulate protein activity and stability.

Structural and functional properties of Escherichia coli-derived nucleoplasmin. A comparative study of recombinant and natural proteins

Fourier transform infrared spectroscopy, circular dichroism and prediction techniques have been used to investigate the conformational properties of nucleoplasmin isolated from oocytes and eggs of Xenopus. laevis and overexpressed in Escherichia coli. A simple and fast method allows purification of recombinant nucleoplasmin free of truncated and/or aggregated forms, and therefore provides a suitable sample to carry out the structural and functional comparison between these proteins. The secondary structure of the three proteins estimated from both spectroscopic techniques was very similar, and was found to be 31--33% loops, 27--34% beta structure, 22--26% turns and 9-14% alpha helix. Prediction studies, in good agreement with experimental data, also suggest that beta structure is the major regular conformation, and that loops and turns are the most abundant conformational features within the secondary structure of nucleoplasmin. Furthermore, the spectroscopic characterization of a truncated version of the protein, lacking 80 residues at the C-terminus, and the prediction data indicate that the secondary structure elements of the protein are segregated into two regions. The N-terminal fragment (comprising residues 1--120) which holds all the putative beta strands, and the solvent-exposed C-terminal region, that is suggested to be enriched in turn and loop structures. The phosphate/protein monomer molar ratios, obtained from chemical analysis and mass spectrometry, are 0, 3 and 7--10 for recombinant, oocyte and egg nucleoplasmin, respectively. Phosphorylation does not significantly affect the secondary structure of the protein, but clearly modulates its ability to decondense sperm nuclei and to remove basic proteins from DNA.