Adaptive immunity depends on major histocompatibility complex class I (MHC I) presentation of peptides, a process orchestrated by the peptide-loading complex (PLC) in the endoplasmic reticulum (ER). The PLC ensures precise peptide selection and loading and is a major target of viral immune evasion, notably by human cytomegalovirus (HCMV). Here, we report the 2.59- to 2.88-Å cryo-electron microscopy structure of native human PLC bound to the HCMV immune evasin US6. US6 inhibits the transporter associated with antigen processing 1/2 (TAP1/2) by laterally attaching its transmembrane helix to TAP2 using a disulfide-rich domain to mimic a translocating peptide. This domain blocks the ER-lumenal exit and locks TAP in an outward-facing conformation with closed nucleotide-binding domains and asymmetric adenosine 5'-triphosphate/adenosine 5'-diphosphate occlusion. The structure also reveals how TAP's amino-terminal transmembrane domains scaffold the MHC I chaperone tapasin. These findings elucidate the mechanism of US6-mediated immune evasion and highlight potential targets for therapeutic modulation of immune presentation in infection and cancer.

Abstract New antimalarial drugs are needed to combat the current emergence and spread of Plasmodium falciparum parasite resistance to artemisinin-based combination therapies. Here, we characterize ZY19489, a triaminopyrimidine presently in a Phase Ib clinical trial. Asexual blood-stage parasites pressured with ZY19489 acquire low-grade resistance, mediated by a novel mutation in the P. falciparum chloroquine resistance transporter (PfCRT) that causes slow growth rates and a substantial fitness cost. ZY19489-resistant parasites lose their chloroquine resistance status and become hypersusceptible to piperaquine (PPQ), an artemisinin-based combination partner drug. Uptake studies in proteoliposomes loaded with drug-resistant PfCRT isoforms demonstrate that ZY19489 can block mutant PfCRT-mediated PPQ and chloroquine transport. In parasites, PfCRT mutant variants can mediate PPQ and chloroquine resistance via their efflux out of the digestive vacuole. Our findings evoke a scenario of an evolutionary trap whereby resistance to ZY19489 can block PPQ and chloroquine efflux and thereby restore their activity. Metabolomic studies show that ZY19489 leads to significantly reduced intracellular levels of short hemoglobin-derived peptides (a natural substrate of PfCRT) and accumulation of pyrimidine deoxynucleotides. Our results present a possible marker for tracking the evolution of clinical resistance to ZY19489 and a rationale for pairing this molecule with PPQ to generate a resistance-refractory combination.

Enzymes that reside in the membrane are responsible for a myriad of vital tasks such as assembly of and changes to the membrane itself, and modification of proteins that reside therein or are secreted through the various cellular compartments. Understanding how these enzymes work at a molecular level is most often dependent on high resolution structural information. While the rates of success for the determination of structures of integral membrane proteins in general, enzymes included, have improved considerably-most notably because of recent advances in single particle cryo-electron microscopy (cryo-EM) technology-considerable challenges to obtaining high resolution structures remain. Without a doubt, the quality of the protein sample is the most critical parameter, where a suitable target must first be identified, then expression and purification conditions optimized. Here, we describe in detail a standard approach and workflow, using the prokaryotic glycosyltransferase GtrB as an example. Together, the methods described here demonstrate that careful selection via thorough screening, and optimization of expression and purification conditions, are an invaluable investment of time, ultimately yielding the best target not only for successful high-resolution structural analyses-X-ray crystallography and cryogenic electron microscopy in this case-but also for biochemical and biophysical studies.

The Mycobacteriales are an order of diverse bacteria that thrive in many environmental and host-associated niches. Because the most notorious member of this clade, Mycobacterium tuberculosis, is a major human pathogen, research on Mycobacteriales has focused on pathogenesis, and, as a consequence, many fundamental aspects of Mycobacterial biology remain understudied. Here, we address this gap by performing a genome-wide CRISPRi chemical genomics screen using a diverse set of >35 antibiotics, detergents, and other anti-microbials predominantly targeting the cell envelope of Mycobacterium smegmatis, a saprophytic model Mycobacterium. We highlight new information derived from this screen, including the identification of novel functions for previously uncharacterized conserved and essential genes (in mycolic acid and arabinogalactan synthesis), the discovery of a new drug scaffold/protein target pair, and insights into the mechanism of action of two commonly used antibiotics. These data are also a valuable resource for the mycobacterial research community, as they provide thousands of novel phenotypes for uncharacterized genes and meaningful phenotypic correlations between annotated and uncharacterized genes.

The genetic basis of Plasmodium falciparum resistance to quinine, a drug used to treat severe malaria, has long been unclear. To investigate this, here we used a human liver-chimaeric mouse model to conduct a P. falciparum genetic cross between quinine-partially resistant and quinine-sensitive parasites. Drug profiling and quantitative trait loci analyses of 120 unique recombinant progeny mapped resistance to segments on chromosomes 7 and 12, indicating a polygenic basis. The chloroquine resistance transporter PfCRT and a structurally similar putative drug/metabolite transporter, DMT1, were identified as primary chromosome 7 candidates based on gene-editing studies. In a proteoliposome assay, both mutant DMT1 and PfCRT transported more quinine than their wild-type isoforms. DMT1 localized to the P. falciparum digestive vacuole, lipid bodies, parasitophorous vacuolar membrane and structures associated with vesicular trafficking. An ATP-dependent zinc metalloprotease (FtsH1) on chromosome 12 also modulated quinine and chloroquine resistance. We suggest that genotypic surveillance of these markers should be performed in clinical settings of quinine use.

New antimalarial drugs are essential to combat the current emergence and spread of Plasmodium falciparum parasite resistance to first-line artemisinin-based combination therapies. Here, we identify a mechanism of parasite resistance to ZY19489, a triaminopyrimidine currently in a Phase IIb clinical trial. Low-grade resistance was mediated by a novel mutation in the P. falciparum chloroquine resistance transporter PfCRT, which caused a major reduction in asexual blood stage parasite growth rates and a substantial fitness cost. Parasites resistant to ZY19489 lost their chloroquine resistance status and became hypersusceptible to the artemisinin-based combination partner drug piperaquine. All three agents were shown to interfere with parasite-mediated catabolism of host hemoglobin. Uptake studies in PfCRT-containing proteoliposomes provide evidence that ZY19489 can block mutant PfCRT-mediated efflux of piperaquine and chloroquine, creating a scenario of an evolutionary trap whereby resistance to ZY19489 blocks PfCRT efflux-mediated resistance and restores susceptibility to piperaquine and chloroquine. Metabolomic studies revealed that ZY19489 significantly reduces intracellular levels of short hemoglobin-derived peptides (a natural substrate of PfCRT) and leads to higher accumulation of pyrimidine deoxynucleotides. Our data present a marker for tracking the evolution of clinical resistance to ZY19489 and a rationale for pairing this with piperaquine to generate a novel resistance-refractory combination.

The emergence of drug-resistant strains exacerbates the global challenge of tuberculosis caused by Mycobacterium tuberculosis (Mtb). Central to the pathogenicity of Mtb is its complex cell envelope, which serves as a barrier against both immune system and pharmacological attacks. Two key components of this envelope, arabinogalactan (AG) and lipoarabinomannan (LAM) are complex polysaccharides that contain integral arabinan domains important for cell wall structural and functional integrity. The arabinofuranosyltransferase AftB terminates the synthesis of these arabinan domains by catalyzing the addition of the addition of β-(1→2)-linked terminal arabinofuranose residues. Here, we present the cryo-EM structures of Mycobacterium chubuense AftB in its apo and donor substrate analog-bound form, determined to 2.9 Å and 3.4 Å resolution, respectively. Our structures reveal that AftB has a GT-C fold transmembrane (TM) domain comprised of eleven TM helices and a periplasmic cap domain. AftB has an irregular tube-shaped cavity that bridges the two proposed substrate binding sites. By integrating structural analysis, biochemical assays, and molecular dynamics simulations, we elucidate the molecular basis of the reaction mechanism of AftB and propose a model for catalysis.

Glycosyltransferases (GTs) catalyze the addition of sugars to diverse substrates facilitating complex glycoconjugate biosynthesis across all domains of life. When embedded in or associated with the membrane, these enzymes often depend on polyisoprenyl-phosphate or -pyrophosphate (PP) lipid carriers, including undecaprenyl phosphate in bacteria and dolichol phosphate in eukaryotes, to transfer glycan moieties. GTs that bind PP substrates (PP-GTs) are functionally diverse but share some common structural features within their family or subfamily, particularly with respect to how they interact with their cognate PP ligands. Recent advances in single-particle cryo-electron microscopy (cryo-EM) have provided insight into the structures of PP-GTs and the modes by which they bind their PP ligands. Here, we explore the structural landscape of PP-GTs, focusing mainly on those for which there is molecular-level information on liganded states, and highlight how PP coordination modalities may be shared or differ among members of this diverse enzyme class.

Polymyxins are used to treat infections caused by multidrug-resistant Gram-negative bacteria. They are cationic peptides that target the negatively charged lipid A component of lipopolysaccharides, disrupting the outer membrane and lysing the cell. Polymyxin resistance is conferred by inner-membrane enzymes, such as phosphoethanolamine transferases, which add positively charged phosphoethanolamine to lipid A. Here, we present the structure of MCR-1, a plasmid-encoded phosphoethanolamine transferase, in its liganded form. The phosphatidylethanolamine donor substrate is bound near the active site in the periplasmic domain, and lipid A is bound over 20 Å away, within the transmembrane region. Integrating structural, biochemical, and drug-resistance data with computational analyses, we propose a two-state model in which the periplasmic domain rotates to bring the active site to lipid A, near the preferential phosphate modification site for MCR-1. This enzymatic mechanism may be generally applicable to other phosphoform transferases with large, globular soluble domains.

Vitamin A is essential for vision and many other biological processes required for human health and survival. Extracellular retinol binding protein (RBP) delivers vitamin A into the cell upon binding to the vitamin A transporter, STRA6. However, when retinol free RBP binds to STRA6, it induces vitamin A transport out of the cell. The bi-directionality of vitamin A transport is thought to be regulated further by an intracellular protein-protein interaction (PPI) between STRA6 and the EF-hand Ca2+-binding protein, calmodulin (CaM). Insights regarding how CaM regulates vitamin A transport were originally provided at atomic resolution by a cryoEM structure of the zebrafish STRA6-CaM complex. This cryoEM structure, together with NMR studies, confirmed that three STRA6 helices (i.e., BP0, BP1, and BP2) comprised the CaM-STRA6 binding interface, with BP2 providing the major set of interactions. NMR and other biophysical methods demonstrated that zebrafish BP2 peptide (zfBP2) binding to CaM involved a Ca2+-dependent type 2 binding and functional folding mechanism of action, which could influence structural, dynamic, and allosteric functions of STRA6. To expand our understanding of vitamin A transport to a mammalian STRA6 transporter, the backbone and sidechain 1HN, 13C, and 15N resonances were assigned here for CaCaM (148 residues) when bound to a sheep BP2 peptide (32 residues) (shBP2). Interestingly, the NMR data showed CaCaM resonances were affected differently upon binding shBP2 versus zfBP2. Such differences may be useful for distinguishing important features regarding CaCaM complexes with mammalian versus zebrafish STRA6.

The genetic basis of Plasmodium falciparum resistance to quinine (QN), a drug used to treat severe malaria, has long been enigmatic. To gain further insight, we used FRG-NOD human liver-chimeric mice to conduct a P. falciparum genetic cross between QN-resistant (Cam3.II) and QN-sensitive (NF54) parasites, which also differ in their susceptibility to chloroquine (CQ). By applying different selective conditions to progeny pools prior to cloning, we recovered 120 unique recombinant progeny. Drug profiling and quantitative trait loci analyses of the progeny revealed predominant peaks on chromosomes 7 and 12 associated with CQ and QN resistance, that is consistent with a multifactorial mechanism of resistance for these compounds. CQ and monodesethyl-CQ (md-CQ) resistance mapped to a chromosome 7 region harboring pfcrt as expected. However, for QN, resistance mapped to a dominant chromosome 7 peak centered 295 kb downstream of pfcrt, with pfcrt showing a smaller peak. We identified the drug/metabolite transporter 1 (DMT1) as the top chromosome 7 candidate due to its structural similarity to PfCRT and proximity to the peak. Deleting DMT1 in QN-resistant Cam3.II parasites significantly sensitized the parasite to QN but not to the other drugs tested, suggesting that DMT1 mediates QN response specifically. We localized DMT1 to structures associated with vesicular trafficking, as well as the parasitophorous vacuolar membrane, lipid bodies, and the digestive vacuole. We also observed that mutant DMT1 transports more QN than the wild-type isoform in vitro. Gene editing confirmed an additional role for mutant PfCRT in mediating QN resistance. In addition, we identified an ATP-dependent zinc metalloprotease (FtsH1) as one of the top candidates in the chromosome 12 locus and confirmed its role as a potential mediator of QN resistance and a modulator of md-CQ resistance using CRISPR/Cas9 SNP-edited lines. Interestingly, this chromosome 12 region mapped to resistance to both CQ and QN and was preferentially co-inherited with pfcrt. Our study demonstrates that DMT1 is a novel marker of QN resistance and that a new chromosome 12 locus associates with CQ and QN response, with ftsh1 as a potential candidate, suggesting these genes in addition to pfcrt should be genotyped in surveillance and clinical settings.

Tuberculosis (TB), a leading cause of death among infectious diseases globally, is caused by Mycobacterium tuberculosis (Mtb). The pathogenicity of Mtb is largely attributed to its complex cell envelope, which includes a class of glycolipids called phosphatidyl-myo-inositol mannosides (PIMs). These glycolipids maintain the integrity of the cell envelope, regulate permeability, and mediate host-pathogen interactions. PIMs comprise a phosphatidyl-myo-inositol core decorated with one to six mannose residues and up to four acyl chains. The mannosyltransferase PimE catalyzes the transfer of the fifth PIM mannose residue from a polyprenyl phosphate-mannose (PPM) donor. This step contributes to the proper assembly and function of the mycobacterial cell envelope; however, the structural basis for substrate recognition and the catalytic mechanism of PimE remain poorly understood. Here, we present the cryo-electron microscopy (cryo-EM) structures of PimE from Mycobacterium abscessus in its apo and product-bound form. The structures reveal a distinctive binding cavity that accommodates both donor and acceptor substrates/products. Key residues involved in substrate coordination and catalysis were identified and validated via in vitro assays and in vivo complementation, while molecular dynamics simulations delineated access pathways and binding dynamics. Our integrated approach provides comprehensive insights into PimE function and informs potential strategies for anti-TB therapeutics.