Butyrophilin-2A1 Directly Binds Germline-Encoded Regions of the Vγ9Vδ2 TCR and Is Essential for Phosphoantigen Sensing.

Vγ9Vδ2 T cells respond in a TCR-dependent fashion to both microbial and host-derived pyrophosphate compounds (phosphoantigens, or P-Ag). Butyrophilin-3A1 (BTN3A1), a protein structurally related to the B7 family of costimulatory molecules, is necessary but insufficient for this process. We performed radiation hybrid screens to uncover direct TCR ligands and cofactors that potentiate BTN3A1's P-Ag sensing function. These experiments identified butyrophilin-2A1 (BTN2A1) as essential to Vγ9Vδ2 T cell recognition. BTN2A1 synergised with BTN3A1 in sensitizing P-Ag-exposed cells for Vγ9Vδ2 TCR-mediated responses. Surface plasmon resonance experiments established Vγ9Vδ2 TCRs used germline-encoded Vγ9 regions to directly bind the BTN2A1 CFG-IgV domain surface. Notably, somatically recombined CDR3 loops implicated in P-Ag recognition were uninvolved. Immunoprecipitations demonstrated close cell-surface BTN2A1-BTN3A1 association independent of P-Ag stimulation. Thus, BTN2A1 is a BTN3A1-linked co-factor critical to Vγ9Vδ2 TCR recognition. Furthermore, these results suggest a composite-ligand model of P-Ag sensing wherein the Vγ9Vδ2 TCR directly interacts with both BTN2A1 and an additional ligand recognized in a CDR3-dependent manner.

Peptidoglycan maturation controls outer membrane protein assembly.

Linkages between the outer membrane of Gram-negative bacteria and the peptidoglycan layer are crucial for the maintenance of cellular integrity and enable survival in challenging environments1-5. The function of the outer membrane is dependent on outer membrane proteins (OMPs), which are inserted into the membrane by the ß-barrel assembly machine6,7 (BAM). Growing Escherichia coli cells segregate old OMPs towards the poles by a process known as binary partitioning, the basis of which is unknown8. Here we demonstrate that peptidoglycan underpins the spatiotemporal organization of OMPs. Mature, tetrapeptide-rich peptidoglycan binds to BAM components and suppresses OMP foldase activity. Nascent peptidoglycan, which is enriched in pentapeptides and concentrated at septa9, associates with BAM poorly and has little effect on its activity, leading to preferential insertion of OMPs at division sites. The synchronization of OMP biogenesis with cell wall growth results in the binary partitioning of OMPs as cells divide. Our study reveals that Gram-negative bacteria coordinate the assembly of two major cell envelope layers by rendering OMP biogenesis responsive to peptidoglycan maturation, a potential vulnerability that could be exploited in future antibiotic design.

The vaccinia chondroitin sulfate binding protein drives host membrane curvature to facilitate fusion.

Cellular attachment of viruses determines their cell tropism and species specificity. For entry, vaccinia, the prototypic poxvirus, relies on four binding proteins and an eleven-protein entry fusion complex. The contribution of the individual virus binding proteins to virion binding orientation and membrane fusion is unclear. Here, we show that virus binding proteins guide side-on virion binding and promote curvature of the host membrane towards the virus fusion machinery to facilitate fusion. Using a membrane-bleb model system together with super-resolution and electron microscopy we find that side-bound vaccinia virions induce membrane invagination in the presence of low pH. Repression or deletion of individual binding proteins reveals that three of four contribute to binding orientation, amongst which the chondroitin sulfate binding protein, D8, is required for host membrane bending. Consistent with low-pH dependent macropinocytic entry of vaccinia, loss of D8 prevents virion-associated macropinosome membrane bending, disrupts fusion pore formation and infection. Our results show that viral binding proteins are active participants in successful virus membrane fusion and illustrate the importance of virus protein architecture for successful infection.

An octameric PqiC toroid stabilises the outer-membrane interaction of the PqiABC transport system.

The E. coli Paraquat Inducible (Pqi) Pathway is a putative Gram-negative phospholipid transport system. The pathway comprises three components: an integral inner membrane protein (PqiA), a periplasmic spanning MCE family protein (PqiB) and an outer membrane lipoprotein (PqiC). Interactions between all complex components, including stoichiometry, remain uncharacterised; nevertheless, once assembled into their quaternary complex, the trio of Pqi proteins are anticipated to provide a continuous channel between the inner and outer membranes of diderms. Here, we present X-ray structures of both the native and a truncated, soluble construct of the PqiC lipoprotein, providing insight into its biological assembly, and utilise neutron reflectometry to characterise the nature of the PqiB-PqiC-membrane interaction. Finally, we employ phenotypic complementation assays to probe specific PqiC residues, which imply the interaction between PqiB and PqiC is less intimate than previously anticipated.

Accurate compound-specific 14C dating of archaeological pottery vessels.

Pottery is one of the most commonly recovered artefacts from archaeological sites. Despite more than a century of relative dating based on typology and seriation1, accurate dating of pottery using the radiocarbon dating method has proven extremely challenging owing to the limited survival of organic temper and unreliability of visible residues2-4. Here we report a method to directly date archaeological pottery based on accelerator mass spectrometry analysis of 14C in absorbed food residues using palmitic (C16:0) and stearic (C18:0) fatty acids purified by preparative gas chromatography5-8. We present accurate compound-specific radiocarbon determinations of lipids extracted from pottery vessels, which were rigorously evaluated by comparison with dendrochronological dates9,10 and inclusion in site and regional chronologies that contained previously determined radiocarbon dates on other materials11-15. Notably, the compound-specific dates from each of the C16:0 and C18:0 fatty acids in pottery vessels provide an internal quality control of the results6 and are entirely compatible with dates for other commonly dated materials. Accurate radiocarbon dating of pottery vessels can reveal: (1) the period of use of pottery; (2) the antiquity of organic residues, including when specific foodstuffs were exploited; (3) the chronology of sites in the absence of traditionally datable materials; and (4) direct verification of pottery typochronologies. Here we used the method to date the exploitation of dairy and carcass products in Neolithic vessels from Britain, Anatolia, central and western Europe, and Saharan Africa.

Dating the emergence of dairying by the first farmers of Central Europe using 14C analysis of fatty acids preserved in pottery vessels.

Direct, accurate, and precise dating of archaeological pottery vessels is now achievable using a recently developed approach based on the radiocarbon dating of purified molecular components of food residues preserved in the walls of pottery vessels. The method targets fatty acids from animal fat residues, making it uniquely suited for directly dating the inception of new food commodities in prehistoric populations. Here, we report a large-scale application of the method by directly dating the introduction of dairying into Central Europe by the Linearbandkeramik (LBK) cultural group based on dairy fat residues. The radiocarbon dates (n = 27) from the 54th century BC from the western and eastern expansion of the LBK suggest dairy exploitation arrived with the first settlers in the respective regions and were not gradually adopted later. This is particularly significant, as contemporaneous LBK sites showed an uneven distribution of dairy exploitation. Significantly, our findings demonstrate the power of directly dating the introduction of new food commodities, hence removing taphonomic uncertainties when assessing this indirectly based on associated cultural materials or other remains.

The lipoprotein DolP affects cell separation in Escherichia coli, but not as an upstream regulator of NlpD.

Bacterial amidases are essential to split the shared envelope of adjunct daughter cells to allow cell separation. Their activity needs to be precisely controlled to prevent cell lysis. In Escherichia coli, amidase activity is controlled by three regulatory proteins NlpD, EnvC and ActS. However, recent studies linked the outer membrane lipoprotein DolP (formerly YraP) as a potential upstream regulator of NlpD. In this study we explored this link in further detail. To our surprise DolP did not modulate amidase activity in vitro and was unable to interact with NlpD in pull-down and MST (MicroScale Thermophoresis) assays. Next, we excluded the hypothesis that ΔdolP phenocopied ΔnlpD in a range of envelope stresses. However, morphological analysis of double deletion mutants of amidases (AmiA, AmiB AmiC) and amidase regulators with dolP revealed that ΔamiAΔdolP and ΔenvCΔdolP mutants display longer chain length compared to their parental strains indicating a role for DolP in cell division. Overall, we present evidence that DolP does not affect NlpD function in vitro, implying that DolP is not an upstream regulator of NlpD. However, DolP may impact daughter cell separation by interacting directly with AmiA or AmiC, or by a yet undiscovered mechanism.

Surface-tethered planar membranes containing the ß-barrel assembly machinery: a platform for investigating bacterial outer membrane protein folding.

The outer membrane of Gram-negative bacteria presents a robust physicochemical barrier protecting the cell from both the natural environment and acting as the first line of defense against antimicrobial materials. The proteins situated within the outer membrane are responsible for a range of biological functions including controlling influx and efflux. These outer membrane proteins (OMPs) are ultimately inserted and folded within the membrane by the ß-barrel assembly machine (Bam) complex. The precise mechanism by which the Bam complex folds and inserts OMPs remains unclear. Here, we have developed a platform for investigating Bam-mediated OMP insertion. By derivatizing a gold surface with a copper-chelating self-assembled monolayer, we were able to assemble a planar system containing the complete Bam complex reconstituted within a phospholipid bilayer. Structural characterization of this interfacial protein-tethered bilayer by polarized neutron reflectometry revealed distinct regions consistent with known high-resolution models of the Bam complex. Additionally, by monitoring changes of mass associated with OMP insertion by quartz crystal microbalance with dissipation monitoring, we were able to demonstrate the functionality of this system by inserting two diverse OMPs within the membrane, pertactin, and OmpT. This platform has promising application in investigating the mechanism of Bam-mediated OMP insertion, in addition to OMP function and activity within a phospholipid bilayer environment.

Iron is a ligand of SecA-like metal-binding domains in vivo.

The ATPase SecA is an essential component of the bacterial Sec machinery, which transports proteins across the cytoplasmic membrane. Most SecA proteins contain a long C-terminal tail (CTT). In Escherichia coli, the CTT contains a structurally flexible linker domain and a small metal-binding domain (MBD). The MBD coordinates zinc via a conserved cysteine-containing motif and binds to SecB and ribosomes. In this study, we screened a high-density transposon library for mutants that affect the susceptibility of E. coli to sodium azide, which inhibits SecA-mediated translocation. Results from sequencing this library suggested that mutations removing the CTT make E. coli less susceptible to sodium azide at subinhibitory concentrations. Copurification experiments suggested that the MBD binds to iron and that azide disrupts iron binding. Azide also disrupted binding of SecA to membranes. Two other E. coli proteins that contain SecA-like MBDs, YecA and YchJ, also copurified with iron, and NMR spectroscopy experiments indicated that YecA binds iron via its MBD. Competition experiments and equilibrium binding measurements indicated that the SecA MBD binds preferentially to iron and that a conserved serine is required for this specificity. Finally, structural modeling suggested a plausible model for the octahedral coordination of iron. Taken together, our results suggest that SecA-like MBDs likely bind to iron in vivo.

Methods for the solubilisation of membrane proteins: the micelle-aneous world of membrane protein solubilisation.

The solubilisation of membrane proteins (MPs) necessitates the overlap of two contradictory events; the extraction of MPs from their native lipid membranes and their subsequent stabilisation in aqueous environments. Whilst the current myriad of membrane mimetic systems provide a range of modus operandi, there are no golden rules for selecting the optimal pipeline for solubilisation of a specific MP hence a miscellaneous approach must be employed balancing both solubilisation efficiency and protein stability. In recent years, numerous diverse lipid membrane mimetic systems have been developed, expanding the pool of available solubilisation strategies. This review provides an overview of recent developments in the membrane mimetic field, with particular emphasis placed upon detergents, polymer-based nanodiscs and amphipols, highlighting the latest reagents to enter the toolbox of MP research.

Development of Alditol Acetate Derivatives for the Determination of 15N-Enriched Amino Sugars by Gas Chromatography-Combustion-Isotope Ratio Mass Spectrometry.

Amino sugars can be used as indices to evaluate the role of soil microorganisms in active nitrogen (N) cycling in soil. This paper details the assessment of the suitability of gas chromatography-combustion-isotope ratio mass spectrometry (GC-C-IRMS) for the analysis of 15N-enriched amino sugars as alditol acetate derivatives prior to application of a novel 15N stable isotope probing (SIP) approach to amino sugars. The efficient derivatization and cleanup of alditol acetate derivatives for GC was achieved using commercially available amino sugars, including glucosamine, mannosamine, galactosamine, and muramic acid, as laboratory standards. A VF-23ms stationary phase was found to produce optimal separations of all four compounds. The structure of the alditol acetate derivatives was confirmed using gas chromatography/mass spectrometry (GC/MS). For GC-C-IRMS determinations, implementation of a two-point normalization confirmed the optimal carrier gas flow rate to be 1.7 mL min-1. Linearity of δ15N value determinations up to δ15Nt of 469 ± 3.1‰ (where δ15Nt is the independently measured δ15N value) was confirmed when 30 nmol N was injected on-column, with the direction of deviation from δ15Nt at low sample amount dependent on the 15N abundance of the analyte. Observed between- and within-run memory effects were significant ( P < 0.007) when a highly enriched standard (469 ± 3.1‰) was run; therefore, analytical run order and variation in 15N enrichment of analytes within the same sample must be considered. The investigated parameters have confirmed the isotopic robustness of alditol acetate derivatives of amino sugars for the GC-C-IRMS analysis of 15N-enriched amino sugars in terms of linearity over an enrichment range (natural abundance to 469 ± 3.1‰) with on-column analyte amount over 30 nmol N.

YraP Contributes to Cell Envelope Integrity and Virulence of Salmonella enterica Serovar Typhimurium.

Mutations in σE-regulated lipoproteins have previously been shown to impact bacterial viability under conditions of stress and during in vivo infection. YraP is conserved across a number of Gram-negative pathogens, including Neisseria meningitidis, where the homolog is a component of the Bexsero meningococcal group B vaccine. Investigations using laboratory-adapted Escherichia coli K-12 have shown that yraP mutants have elevated sensitivity to a range of compounds, including detergents and normally ineffective antibiotics. In this study, we investigate the role of the outer membrane lipoprotein YraP in the pathogenesis of Salmonella enterica serovar Typhimurium. We show that mutations in S Typhimurium yraP result in a defective outer membrane barrier with elevated sensitivity to a range of compounds. This defect is associated with attenuated virulence in an oral infection model and during the early stages of systemic infection. We show that this attenuation is not a result of defects in lipopolysaccharide and O-antigen synthesis, changes in outer membrane protein levels, or the ability to adhere to and invade eukaryotic cell lines in vitro.

Practical Considerations in High-Precision Compound-Specific Radiocarbon Analyses: Eliminating the Effects of Solvent and Sample Cross-Contamination on Accuracy and Precision.

Preparative capillary gas chromatography (pcGC) is widely used for the isolation of single compounds for radiocarbon determinations. While being effective at isolating compounds, there are still genuine concerns relating to contamination associated with the isolation procedure, such as incomplete removal of solvent used to recover isolated compounds from the traps and cross-contamination, which can lead to erroneous 14C determinations. Herein we describe new approaches to identifying and removing these two sources of contamination. First, we replaced the common "U" trap design, which requires recovery of compounds using organic solvent, with a novel solventless trapping system (STS), consisting of a simple glass tube containing a glass wool plug, allowing condensation of a target compound in the wool and its solventless recovery by pushing the glass wool directly into a foil capsule for graphitization. With the STS trap, an average of 95.7% of the target compound was recovered, and contamination from column bleed was reduced. In addition, comparison of 14C determinations of fatty acid methyl ester (FAME) standards determined offline to those isolated by pcGC in STS traps showed excellent reproducibility and accuracy compared to those isolated using the commercial "U" traps. Second, "coldspots" were identified in the instrument, i.e., the termini of capillaries in the preparative unit, which can be cleaned of compounds condensed from earlier runs using a heat gun. Our new procedure, incorporating these two modifications, was tested on archeological fat hoards, producing 14C dates on isolated C16:0 and C18:0 fatty acids statistically consistent with the bulk dates of the archeological material.

Minichaperone (GroEL191-345) mediated folding of MalZ proceeds by binding and release of native and functional intermediates.

The isolated apical domain of GroEL consisting of residues 191-345 (known as "minichaperone") binds and assists the folding of a wide variety of client proteins without GroES and ATP, but the mechanism of its action is still unknown. In order to probe into the matter, we have examined minichaperone-mediated folding of a large aggregation prone protein Maltodextrin-glucosidase (MalZ). The key objective was to identify whether MalZ exists free in solution, or remains bound to, or cycling on and off the minichaperone during the refolding process. When GroES was introduced during refolding process, production of the native MalZ was inhibited. We also observed the same findings with a trap mutant of GroEL, which stably captures a predominantly non-native MalZ released from minichaperone during refolding process, but does not release it. Tryptophan and ANS fluorescence measurements indicated that refolded MalZ has the same structure as the native MalZ, but that its structure when bound to minichaperone is different. Surface plasmon resonance measurements provide an estimate for the equilibrium dissociation constant KD for the MalZ-minichaperone complex of 0.21 ±â€¯0.04 µM, which are significantly higher than for most GroEL clients. This showed that minichaperone interacts loosely with MalZ to allow the protein to change its conformation and fold while bound during the refolding process. These observations suggest that the minichaperone works by carrying out repeated cycles of binding aggregation-prone protein MalZ in a relatively compact conformation and in a partially folded but active state, and releasing them to attempt to fold in solution.

Elemental Composition at Silicone Hydrogel Contact Lens Surfaces.

OBJECTIVES: The outermost surface composition of 11 silicone hydrogel (SiHy) lenses was measured using X-ray photoelectron spectroscopy (XPS) to understand differences in wettability and potential interactions within an ocular environment. The SiHy lenses tested included balafilcon A, lotrafilcon A, lotrafilcon B, senofilcon A, comfilcon A, and somofilcon A reusable 2-week or monthly replacement lenses and delefilcon A, samfilcon A, narafilcon A, stenfilcon A, and somofilcon A daily disposable lenses. METHODS: All lenses were soaked for 24 hr in phosphate-buffered saline to remove all packaging solution and dried under vacuum overnight before analysis. X-ray photoelectron spectroscopy measurements were performed at 2 take-off angles, 55° and 75°, to evaluate changes in elemental composition as a function of depth from the surface. RESULTS: Detailed analysis of the XPS data revealed distinct differences in the chemical makeup of the different lens types. For all lenses, carbon, oxygen, and nitrogen were observed in varying quantities. In addition, fluorine was detected at the outermost surface region of comfilcon A (3.4%) and lotrafilcon A and B (<0.5%). The silicon content of the near-surface region analyzed varied among lens types, ranging from a low of 1.6% (lotrafilcon B) to a high of 16.5% (comfilcon A). In most instances, silicon enrichment at the outermost surface was observed, resulting from differences in lens formulation and design. CONCLUSIONS: Lenses differed most in their surface silicon concentration, with lotrafilcon B and delefilcon A exhibiting the lowest silicon contents and comfilcon A lens exhibiting the highest. Silicon has hydrophobic properties, which, when found at the surface, may influence the wettability of the contact lenses and their interaction with the tear film and ocular tissues. Higher surface silicon contents have been previously correlated with adverse effects, such as enhanced lipid uptake, thus underscoring the importance of monitoring their presence.

Characterization of a Putative Receptor Binding Surface on Skint-1, a Critical Determinant of Dendritic Epidermal T Cell Selection.

Dendritic epidermal T cells (DETC) form a skin-resident γδ T cell population that makes key contributions to cutaneous immune stress surveillance, including non-redundant contributions to protection from cutaneous carcinogens. How DETC become uniquely associated with the epidermis was in large part solved by the identification of Skint-1, the prototypic member of a novel B7-related multigene family. Expressed only by thymic epithelial cells and epidermal keratinocytes, Skint-1 drives specifically the development of DETC progenitors, making it the first clear candidate for a selecting ligand for non-MHC/CD1-restricted T cells. However, the molecular mechanisms underpinning Skint-1 activity are unresolved. Here, we provide evidence that DETC selection requires Skint-1 expression on the surface of thymic epithelial cells, and depends upon specific residues on the CDR3-like loop within the membrane-distal variable domain of Skint-1 (Skint-1 DV). Nuclear magnetic resonance of Skint-1 DV revealed a core tertiary structure conserved across the Skint family, but a highly distinct surface charge distribution, possibly explaining its unique function. Crucially, the CDR3-like loop formed an electrostatically distinct surface, featuring key charged and hydrophobic solvent-exposed residues, at the membrane-distal tip of DV. These results provide the first structural insights into the Skint family, identifying a putative receptor binding surface that directly implicates Skint-1 in receptor-ligand interactions crucial for DETC selection.

Use of a 700 MHz NMR Microcryoprobe for the Identification and Quantification of Exogenous Carbon in Compounds Purified by Preparative Capillary Gas Chromatography for Radiocarbon Determinations.

Preparative capillary gas chromatography (PCGC) is the central technique used for the purification of volatile or semivolatile organic compounds for radiocarbon analysis using accelerator mass spectrometry (AMS). While thicker film columns offer efficient separations, cyclic poly(dimethylsiloxanes) (PDMS) derived from the column's stationary phase have been highlighted as a potential source of contaminant carbon in "trapped" compounds. The PDMS CH3 groups are of "infinite" radiocarbon age due to the fossil carbon origin of the feedstock used in production. Hence, column bleed, if present at sufficiently high concentrations, would shift the radiocarbon ages of trapped compounds to older ages. Quantification of the column bleed in trapped samples, however, is extremely challenging and up to now has only been achieved through indirect 14C determinations of chromatographic blanks, which are used for post 14C determination "corrections". As part of wider investigations aimed at better understanding the chemical nature of contamination in compound-specific 14C determinations, herein, we report a rigorous approach to column bleed identification and quantification. Using reference fatty acid methyl esters (FAMEs), 1H nuclear magnetic resonance spectroscopy (NMR), employing a 700 MHz instrument equipped with a 1.7 mm microcryoprobe optimized for 1H observation, was able to detect low submicrogram amounts of low molecular weight compounds (<500 Da). Direct quantification of PCGC "trapped" FAMEs was achieved based on the recorded 1H NMR spectra. Gravimetrically prepared calibration mixtures of cyclic PMDSs and FAMEs showed column bleed abundance to be below 0.03% w/w of the "trapped" FAMEs, which would lead to a maximum shift in radiocarbon age of <3 years toward older values. We therefore conclude that column bleed contamination has a negligible effect on the 14C determination of FAMEs prepared using the chromatographic method described. The 1H NMR analysis also revealed the absence of other protonated carbon-containing components that would affect radiocarbon determinations at the precisions achievable by AMS.

A novel pathway for outer membrane protein biogenesis in Gram-negative bacteria.

The understanding of the biogenesis of the outer membrane of Gram-negative bacteria is of critical importance due to the emergence of bacteria that are becoming resistant to available antibiotics. A problem that is most serious for Gram-negative bacteria, with essentially few antibiotics under development or likely to be available for clinical use in the near future. The understanding of the Gram-negative bacterial outer membrane is therefore critical to developing new antimicrobial agents, as this membrane makes direct contact with the external milieu, and the proteins present within this membrane are the instruments of microbial warfare, playing key roles in microbial pathogenesis, virulence and multidrug resistance. To date, a single outer membrane complex has been identified as essential for the folding and insertion of proteins into the outer membrane, this is the ß-barrel assembly machine (BAM) complex, which in some cases is supplemented by the Translocation and Assembly Module (TAM). In this issue of Molecular Microbiology, Dunstan et al. have identified a novel pathway for the insertion of a subset of integral membrane proteins into the Gram-negative outer membrane that is independent of the BAM complex and TAM.

Cross-species chimeras reveal BamA POTRA and ß-barrel domains must be fine-tuned for efficient OMP insertion.

BAM is a conserved molecular machine, the central component of which is BamA. Orthologues of BamA are found in all Gram-negative bacteria, chloroplasts and mitochondria where it is required for the folding and insertion of ß-barrel containing integral outer membrane proteins (OMPs) into the outer membrane. BamA binds unfolded ß-barrel precursors via the five polypeptide transport-associated (POTRA) domains at its N-terminus. The C-terminus of BamA folds into a ß-barrel domain, which tethers BamA to the outer membrane and is involved in OMP insertion. BamA orthologues are found in all Gram-negative bacteria and appear to function in a species-specific manner. Here we investigate the nature of this species-specificity by examining whether chimeric Escherichia coli BamA fusion proteins, carrying either the ß-barrel or POTRA domains from various BamA orthologues, can functionally replace E. coli BamA. We demonstrate that the ß-barrel domains of many BamA orthologues are functionally interchangeable. We show that defects in the orthologous POTRA domains can be rescued by compensatory mutations within the ß-barrel. These data reveal that the POTRA and barrel domains must be precisely aligned to ensure efficient OMP insertion.

Evolutionary history of copy-number-variable locus for the low-affinity Fcγ receptor: mutation rate, autoimmune disease, and the legacy of helminth infection.

Both sequence variation and copy-number variation (CNV) of the genes encoding receptors for immunoglobulin G (Fcγ receptors) have been genetically and functionally associated with a number of autoimmune diseases. However, the molecular nature and evolutionary context of this variation is unknown. Here, we describe the structure of the CNV, estimate its mutation rate and diversity, and place it in the context of the known functional alloantigen variation of these genes. Deletion of Fcγ receptor IIIB, associated with systemic lupus erythematosus, is a result of independent nonallelic homologous recombination events with a frequency of approximately 0.1%. We also show that pathogen diversity, in particular helminth diversity, has played a critical role in shaping the functional variation at these genes both between mammalian species and between human populations. Positively selected amino acids are involved in the interaction with IgG and include some amino acids that are known polymorphic alloantigens in humans. This supports a genetic contribution to the hygiene hypothesis, which states that past evolution in the context of helminth diversity has left humans with an array of susceptibility alleles for autoimmune disease in the context of a helminth-free environment. This approach shows the link between pathogens and autoimmune disease at the genetic level and provides a strategy for interrogating the genetic variation underlying autoimmune-disease risk and infectious-disease susceptibility.