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1.
Structure ; 32(8): 1174-1183.e5, 2024 Aug 08.
Artículo en Inglés | MEDLINE | ID: mdl-38776922

RESUMEN

Chemokine receptors belong to the large class of G protein-coupled receptors (GPCRs) and are involved in a number of (patho)physiological processes. Previous studies highlighted the importance of membrane lipids for modulating GPCR structure and function. However, the underlying mechanisms of how lipids regulate GPCRs are often poorly understood. Here, we report that anionic lipid bilayers increase the binding affinity of the chemokine CXCL12 for the atypical chemokine receptor 3 (ACKR3) by modulating the CXCL12 binding kinetics. Notably, the anionic bilayer favors CXCL12 over the more positively charged chemokine CXCL11, which we explained by bilayer interactions orienting CXCL12 but not CXCL11 for productive ACKR3 binding. Furthermore, our data suggest a stabilization of active ACKR3 conformations in anionic bilayers. Taken together, the described regulation of chemokine selectivity of ACKR3 by the lipid bilayer proposes an extended version of the classical model of chemokine binding including the lipid environment of the receptor.


Asunto(s)
Quimiocina CXCL12 , Membrana Dobles de Lípidos , Unión Proteica , Receptores CXCR , Membrana Dobles de Lípidos/metabolismo , Membrana Dobles de Lípidos/química , Humanos , Receptores CXCR/metabolismo , Receptores CXCR/química , Receptores CXCR/genética , Quimiocina CXCL12/metabolismo , Quimiocina CXCL12/química , Quimiocina CXCL11/metabolismo , Quimiocina CXCL11/química , Sitios de Unión , Ligandos , Cinética , Modelos Moleculares
2.
bioRxiv ; 2023 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-37961571

RESUMEN

Canonical chemokine receptor CXCR4 and atypical receptor ACKR3 both respond to CXCL12 but induce different intracellular effector responses to regulate cell migration: CXCR4 couples to G proteins and arrestins, while ACKR3 is arrestin-biased. CXCR4 also signals only in response to CXCL12, whereas ACKR3 recruits ß-arrestin in response to CXCL12, CXCL12 variants, and other peptides and proteins. To investigate the role of conformational dynamics in the distinct pharmacological behaviors of CXCR4 and ACKR3, we utilized single-molecule FRET. The data revealed that apo CXCR4 preferentially populates a high-FRET inactive state while apo ACKR3 shows little conformational preference, consistent with its promiscuous ligand recognition and propensity for activation. Markedly different conformational landscapes of the receptors in response to ligands suggest that activation of ACKR3 may be achieved by a broader distribution of conformational states than CXCR4. The dynamic properties of ACKR3 may also underly its inability to couple to G proteins, making it arrestin-biased.

3.
Extremophiles ; 28(1): 6, 2023 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-38036917

RESUMEN

This study investigated the metabolism of Geobacillus sp. LC300, a promising biorefinery host organism with high substrate utilization rates. A new defined medium was designed and tested that allows for exponential growth to elevated cell densities suitable for quantitative physiological studies. Screening of the metabolic requirements of G. sp. LC300 revealed prototrophy for all essential amino acids and most vitamins and only showed auxotrophy for vitamin B12 and biotin. The effect of temperature and pH on growth rate was investigated, adjusting the optimal growth temperature to several degrees lower than previously reported. Lastly, studies on carbon source utilization revealed a capability for fast growth on several common carbon sources, including monosaccharides, oligosaccharides, and polysaccharides, and the highest ever reported growth rate in defined medium on glucose (2.20 h-1) or glycerol (1.95 h-1). These findings provide a foundation for further exploration of G. sp. LC300's physiology and metabolic regulation, and its potential use in bioproduction processes.


Asunto(s)
Geobacillus , Geobacillus/metabolismo , Carbono/metabolismo , Temperatura , Glucosa/metabolismo
4.
bioRxiv ; 2023 Jul 19.
Artículo en Inglés | MEDLINE | ID: mdl-37502840

RESUMEN

Atypical chemokine receptor 3 (ACKR3, also known as CXCR7) is a scavenger receptor that regulates extracellular levels of the chemokine CXCL12 to maintain responsiveness of its partner, the G protein-coupled receptor (GPCR), CXCR4. ACKR3 is notable because it does not couple to G proteins and instead is completely biased towards arrestins. Our previous studies revealed that GRK2 and GRK5 install distinct distributions of phosphates (or "barcodes") on the ACKR3 carboxy terminal tail, but how these unique barcodes drive different cellular outcomes is not understood. It is also not known if arrestin2 (Arr2) and 3 (Arr3) bind to these barcodes in distinct ways. Here we report cryo-electron microscopy structures of Arr2 and Arr3 in complex with ACKR3 phosphorylated by either GRK2 or GRK5. Unexpectedly, the finger loops of Arr2 and 3 directly insert into the detergent/membrane instead of the transmembrane core of ACKR3, in contrast to previously reported "core" GPCR-arrestin complexes. The distance between the phosphorylation barcode and the receptor transmembrane core regulates the interaction mode of arrestin, alternating between a tighter complex for GRK5 sites and heterogenous primarily "tail only" complexes for GRK2 sites. Arr2 and 3 bind at different angles relative to the core of ACKR3, likely due to differences in membrane/micelle anchoring at their C-edge loops. Our structural investigations were facilitated by Fab7, a novel Fab that binds both Arr2 and 3 in their activated states irrespective of receptor or phosphorylation status, rendering it a potentially useful tool to aid structure determination of any native GPCR-arrestin complex. The structures provide unprecedented insight into how different phosphorylation barcodes and arrestin isoforms can globally affect the configuration of receptor-arrestin complexes. These differences may promote unique downstream intracellular interactions and cellular responses. Our structures also suggest that the 100% bias of ACKR3 for arrestins is driven by the ability of arrestins, but not G proteins, to bind GRK-phosphorylated ACKR3 even when excluded from the receptor cytoplasmic binding pocket.

5.
Cell Mol Life Sci ; 80(2): 55, 2023 Feb 02.
Artículo en Inglés | MEDLINE | ID: mdl-36729338

RESUMEN

Chemokine ligands and receptors regulate the directional migration of leukocytes. Post-translational modifications of chemokine receptors including O-glycosylation and tyrosine sulfation have been reported to regulate ligand binding and resulting signaling. Through in silico analyses, we determined potential conserved O-glycosylation and sulfation sites on human and murine CC chemokine receptors. Glyco-engineered CHO cell lines were used to measure the impact of O-glycosylation on CC chemokine receptor CCR5, while mutation of tyrosine residues and treatment with sodium chlorate were performed to determine the effect of tyrosine sulfation. Changing the glycosylation or tyrosine sulfation on CCR5 reduced the receptor signaling by the more positively charged CCL5 and CCL8 more profoundly compared to the less charged CCL3. The loss of negatively charged sialic acids resulted only in a minor effect on CCL3-induced signal transduction. The enzymes GalNAc-T1 and GalNAc-T11 were shown to be involved in the process of chemokine receptor O-glycosylation. These results indicate that O-glycosylation and tyrosine sulfation are involved in the fine-tuning and recognition of chemokine interactions with CCR5 and the resulting signaling.


Asunto(s)
Quimiocinas , Transducción de Señal , Cricetinae , Animales , Humanos , Ratones , Quimiocinas/metabolismo , Procesamiento Proteico-Postraduccional , Receptores CCR5/genética , Células CHO , Tirosina/metabolismo , Unión Proteica
6.
Metab Eng Commun ; 15: e00212, 2022 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-36425956

RESUMEN

Thermophilic microorganisms show high potential for use as biorefinery cell factories. Their high growth temperatures provide fast conversion rates, lower risk of contaminations, and facilitated purification of volatile products. To date, only a few thermophilic species have been utilized for microbial production purposes, and the development of production strains is impeded by the lack of metabolic engineering tools. In this study, we constructed a genome-scale metabolic model, an important part of the metabolic engineering pipeline, of the fast-growing thermophile Geobacillus sp. LC300. The model (iGEL604) contains 604 genes, 1249 reactions and 1311 metabolites, and the reaction reversibility is based on thermodynamics at the optimum growth temperature. The growth phenotype is analyzed by batch cultivations on two carbon sources, further closing balances in carbon and degree-of-reduction. The predictive ability of the model is benchmarked against experimentally determined growth characteristics and internal flux distributions, showing high similarity to experimental phenotypes.

7.
Sci Adv ; 8(28): eabn8063, 2022 07 15.
Artículo en Inglés | MEDLINE | ID: mdl-35857509

RESUMEN

Both CXC chemokine receptor 4 (CXCR4) and atypical chemokine receptor 3 (ACKR3) are activated by the chemokine CXCL12 yet evoke distinct cellular responses. CXCR4 is a canonical G protein-coupled receptor (GPCR), whereas ACKR3 is intrinsically biased for arrestin. The molecular basis for this difference is not understood. Here, we describe cryo-EM structures of ACKR3 in complex with CXCL12, a more potent CXCL12 variant, and a small-molecule agonist. The bound chemokines adopt an unexpected pose relative to those established for CXCR4 and observed in other receptor-chemokine complexes. Along with functional studies, these structures provide insight into the ligand-binding promiscuity of ACKR3, why it fails to couple to G proteins, and its bias toward ß-arrestin. The results lay the groundwork for understanding the physiological interplay of ACKR3 with other GPCRs.


Asunto(s)
Receptores CXCR4 , Transducción de Señal , Arrestina , Unión Proteica , Receptores CXCR4/metabolismo , beta-Arrestinas/metabolismo
8.
Cells ; 11(8)2022 04 13.
Artículo en Inglés | MEDLINE | ID: mdl-35455996

RESUMEN

Chemokine receptors are extensively involved in a broad range of physiological and pathological processes, making them attractive drug targets. However, despite considerable efforts, there are very few approved drugs targeting this class of seven transmembrane domain receptors to date. In recent years, the importance of including binding kinetics in drug discovery campaigns was emphasized. Therefore, kinetic insight into chemokine-chemokine receptor interactions could help to address this issue. Moreover, it could additionally deepen our understanding of the selectivity and promiscuity of the chemokine-chemokine receptor network. Here, we describe the application, optimization and validation of a homogenous Scintillation Proximity Assay (SPA) for real-time kinetic profiling of chemokine-chemokine receptor interactions on the example of ACKR3 and CXCL12. The principle of the SPA is the detection of radioligand binding to receptors reconstituted into nanodiscs by scintillation light. No receptor modifications are required. The nanodiscs provide a native-like environment for receptors and allow for full control over bilayer composition and size. The continuous assay format enables the monitoring of binding reactions in real-time, and directly accounts for non-specific binding and potential artefacts. Minor adaptations additionally facilitate the determination of equilibrium binding metrics, making the assay a versatile tool for the study of receptor-ligand interactions.


Asunto(s)
Cinética , Ligandos , Unión Proteica , Dominios Proteicos
9.
Sci Signal ; 15(724): eabg7042, 2022 03 08.
Artículo en Inglés | MEDLINE | ID: mdl-35258997

RESUMEN

Extensive ligand-receptor promiscuity in the chemokine signaling system balances beneficial redundancy and specificity. However, this feature poses a major challenge to selectively modulate the system pharmacologically. Here, we identified a conserved cluster of three aromatic receptor residues that anchors the second extracellular loop (ECL2) to the top of receptor transmembrane helices (TM) 4 and 5 and enables recognition of both shared and specific characteristics of interacting chemokines. This cluster was essential for the activation of several chemokine receptors. Furthermore, characteristic motifs of the ß1 strand and 30s loop make the two main CC-chemokine subgroups-the macrophage inflammatory proteins (MIPs) and monocyte chemoattractant proteins (MCPs)-differentially dependent on this cluster in the promiscuous receptors CCR1, CCR2, and CCR5. The cluster additionally enabled CCR1 and CCR5 to discriminate between closely related MIPs based on the N terminus of the chemokine. G protein signaling and ß-arrestin2 recruitment assays confirmed the importance of the conserved cluster in receptor discrimination of chemokine ligands. This extracellular site may facilitate the development of chemokine-related therapeutics.


Asunto(s)
Quimiocinas , Receptores de Quimiocina , Quimiocinas/metabolismo , Ligandos , Estructura Secundaria de Proteína , Receptores CCR5/metabolismo , Receptores de Quimiocina/genética , Receptores de Quimiocina/metabolismo , Transducción de Señal
10.
Elife ; 102021 05 12.
Artículo en Inglés | MEDLINE | ID: mdl-33978571

RESUMEN

Phospholamban (PLN) is a mini-membrane protein that directly controls the cardiac Ca2+-transport response to ß-adrenergic stimulation, thus modulating cardiac output during the fight-or-flight response. In the sarcoplasmic reticulum membrane, PLN binds to the sarco(endo)plasmic reticulum Ca2+-ATPase (SERCA), keeping this enzyme's function within a narrow physiological window. PLN phosphorylation by cAMP-dependent protein kinase A or increase in Ca2+ concentration reverses the inhibitory effects through an unknown mechanism. Using oriented-sample solid-state NMR spectroscopy and replica-averaged NMR-restrained structural refinement, we reveal that phosphorylation of PLN's cytoplasmic regulatory domain signals the disruption of several inhibitory contacts at the transmembrane binding interface of the SERCA-PLN complex that are propagated to the enzyme's active site, augmenting Ca2+ transport. Our findings address long-standing questions about SERCA regulation, epitomizing a signal transduction mechanism operated by posttranslationally modified bitopic membrane proteins.


Asunto(s)
Regulación Alostérica , Proteínas de Unión al Calcio/química , Fosforilación , ATPasas Transportadoras de Calcio del Retículo Sarcoplásmico/química , Animales , Calcio/metabolismo , Proteínas de Unión al Calcio/metabolismo , Escherichia coli , Espectroscopía de Resonancia Magnética , Proteínas de la Membrana/metabolismo , Estructura Molecular , Conformación Proteica , Conejos , Retículo Sarcoplasmático , ATPasas Transportadoras de Calcio del Retículo Sarcoplásmico/metabolismo , Transducción de Señal
11.
AMB Express ; 10(1): 184, 2020 Oct 17.
Artículo en Inglés | MEDLINE | ID: mdl-33068215

RESUMEN

Valorisation of food residues would greatly benefit from development of robust processes that create added value compared to current feed- and biogas applications. Recent advances in membrane-bioreactor-based open mixed microbial cultures, enable robust conversion of fluctuating streams of food residues to a mixture of volatile fatty acids (VFAs). In this study, such a mixed stream of VFAs was investigated as a substrate for Escherichia coli, a well-studied organism suitable for application in further conversion of the acids into compounds of higher value, and/or that are easier to separate from the aqueous medium. E. coli was cultured in batch on a VFA-rich anaerobic digest of food residues, tolerating up to 40 mM of total VFAs without any reduction in growth rate. In carbon-limited chemostats of E. coli W3110 ΔFadR on a simulated VFA mixture, the straight-chain VFAs (C2-C6) in the mixture were readily consumed simultaneously. At a dilution rate of 0.1 h-1, mainly acetic-, propionic- and caproic acid were consumed, while consumption of all the provided acids were observed at 0.05 h-1. Interestingly, also the branched isovaleric acid was consumed through a hitherto unknown mechanism. In total, up to 80% of the carbon from the supplied VFAs was consumed by the cells, and approximately 2.7% was excreted as nucleotide precursors in the medium. These results suggest that VFAs derived from food residues are a promising substrate for E. coli.

12.
J Leukoc Biol ; 107(6): 1123-1135, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-32374043

RESUMEN

Chemokines play critical roles in numerous physiologic and pathologic processes through their action on seven-transmembrane (TM) receptors. The N-terminal domain of chemokines, which is a key determinant of signaling via its binding within a pocket formed by receptors' TM helices, can be the target of proteolytic processing. An illustrative case of this regulatory mechanism is the natural processing of CXCL12 that generates chemokine variants lacking the first two N-terminal residues. Whereas such truncated variants behave as antagonists of CXCR4, the canonical G protein-coupled receptor of CXCL12, they are agonists of the atypical chemokine receptor 3 (ACKR3/CXCR7), suggesting the implication of different structural determinants in the complexes formed between CXCL12 and its two receptors. Recent analyses have suggested that the CXCL12 N-terminus first engages the TM helices of ACKR3 followed by the receptor N-terminus wrapping around the chemokine core. Here we investigated the first stage of ACKR3-CXCL12 interactions by comparing the activity of substituted or N-terminally truncated variants of CXCL12 toward CXCR4 and ACKR3. We showed that modification of the first two N-terminal residues of the chemokine (K1R or P2G) does not alter the ability of CXCL12 to activate ACKR3. Our results also identified the K1R variant as a G protein-biased agonist of CXCR4. Comparative molecular dynamics simulations of the complexes formed by ACKR3 either with CXCL12 or with the P2G variant identified interactions between the N-terminal 2-4 residues of CXCL12 and a pocket formed by receptor's TM helices 2, 6, and 7 as critical determinants for ACKR3 activation.


Asunto(s)
Quimiocina CXCL12/química , AMP Cíclico/química , Receptores CXCR4/química , Receptores CXCR/química , Secuencia de Aminoácidos , Bencilaminas , Sitios de Unión , Quimiocina CXCL11/química , Quimiocina CXCL11/genética , Quimiocina CXCL11/metabolismo , Quimiocina CXCL12/genética , Quimiocina CXCL12/metabolismo , Ciclamas , AMP Cíclico/metabolismo , Expresión Génica , Células HEK293 , Compuestos Heterocíclicos/química , Compuestos Heterocíclicos/farmacología , Humanos , Simulación de Dinámica Molecular , Mutación , Oligopéptidos/química , Oligopéptidos/farmacología , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Receptores CXCR/genética , Receptores CXCR/metabolismo , Receptores CXCR4/antagonistas & inhibidores , Receptores CXCR4/genética , Receptores CXCR4/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , beta-Arrestinas/genética , beta-Arrestinas/metabolismo
13.
PLoS Biol ; 18(4): e3000656, 2020 04.
Artículo en Inglés | MEDLINE | ID: mdl-32271748

RESUMEN

Chemokines and their receptors are orchestrators of cell migration in humans. Because dysregulation of the receptor-chemokine system leads to inflammation and cancer, both chemokines and receptors are highly sought therapeutic targets. Yet one of the barriers for their therapeutic targeting is the limited understanding of the structural principles behind receptor-chemokine recognition and selectivity. The existing structures do not include CXC subfamily complexes and lack information about the receptor distal N-termini, despite the importance of the latter in signaling, regulation, and bias. Here, we report the discovery of the geometry of the complex between full-length CXCR4, a prototypical CXC receptor and driver of cancer metastasis, and its endogenous ligand CXCL12. By comprehensive disulfide cross-linking, we establish the existence and the structure of a novel interface between the CXCR4 distal N-terminus and CXCL12 ß1-strand, while also recapitulating earlier findings from nuclear magnetic resonance, modeling and crystallography of homologous receptors. A cross-linking-informed high-resolution model of the CXCR4-CXCL12 complex pinpoints the interaction determinants and reveals the occupancy of the receptor major subpocket by the CXCL12 proximal N terminus. This newly found positioning of the chemokine proximal N-terminus provides a structural explanation of CXC receptor-chemokine selectivity against other subfamilies. Our findings challenge the traditional two-site understanding of receptor-chemokine recognition, suggest the possibility of new affinity and signaling determinants, and fill a critical void on the structural map of an important class of therapeutic targets. These results will aid the rational design of selective chemokine-receptor targeting small molecules and biologics with novel pharmacology.


Asunto(s)
Quimiocina CXCL12/química , Quimiocina CXCL12/metabolismo , Receptores CXCR4/química , Receptores CXCR4/metabolismo , Animales , Sitios de Unión , Western Blotting , Quimiocina CXCL12/genética , Cisteína/química , Cisteína/genética , Disulfuros/química , Citometría de Flujo , Células HEK293 , Humanos , Insectos/citología , Modelos Moleculares , Mutación , Conformación Proteica , Dominios y Motivos de Interacción de Proteínas , Receptores CXCR4/genética , beta-Arrestinas/metabolismo
14.
J Leukoc Biol ; 107(6): 1115-1122, 2020 06.
Artículo en Inglés | MEDLINE | ID: mdl-31965639

RESUMEN

Chemokines are small soluble proteins that drive cell migration through the formation of concentration gradients. Chemokine binding to G protein-coupled chemokine receptors in the cell membrane activates intracellular signaling pathways and is a fundamental process involved in numerous physiological and pathophysiological functions. In the past few years, significant experimental developments have made it possible to characterize complexes between chemokine receptors and chemokines at a molecular level. Here, I review these developments from an experimental perspective, focusing on how the ability to express, purify, and stabilize receptor:chemokine complexes have made studies by X-ray crystallography, nuclear magnetic resonance, and other methods possible. I give examples of how these studies have advanced our understanding of the architecture of receptor:chemokine complexes as well as the mechanisms involved in complex formation. Finally, I discuss some of the many remaining questions and challenges that will require studies of more receptors and chemokines as well as further development of experimental methods.


Asunto(s)
Quimiocinas/química , Glicosaminoglicanos/química , Receptores de Quimiocina/química , Sitios de Unión , Quimiocinas/genética , Quimiocinas/metabolismo , Cristalografía por Rayos X/métodos , Expresión Génica , Glicosaminoglicanos/metabolismo , Células HEK293 , Humanos , Modelos Moleculares , Resonancia Magnética Nuclear Biomolecular/métodos , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Receptores de Quimiocina/genética , Receptores de Quimiocina/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Transducción de Señal
15.
Sci Signal ; 12(598)2019 09 10.
Artículo en Inglés | MEDLINE | ID: mdl-31506383

RESUMEN

Chemokines bind to membrane-spanning chemokine receptors, which signal through G proteins and promote cell migration. However, atypical chemokine receptor 3 (ACKR3) does not appear to couple to G proteins, and instead of directly promoting cell migration, it regulates the extracellular concentration of chemokines that it shares with the G protein-coupled receptors (GPCRs) CXCR3 and CXCR4, thereby influencing the responses of these receptors. Understanding how these receptors bind their ligands is important for understanding these different processes. Here, we applied association and dissociation kinetic measurements coupled to ß-arrestin recruitment assays to investigate ACKR3:chemokine interactions. Our results showed that CXCL12 binding is unusually slow and driven by the interplay between multiple binding epitopes. We also found that the amino terminus of the receptor played a key role in chemokine binding and activation by preventing chemokine dissociation. It was thought that chemokines initially bind receptors through interactions between the globular domain of the chemokine and the receptor amino terminus, which then guides the chemokine amino terminus into the transmembrane pocket of the receptor to initiate signaling. On the basis of our kinetic data, we propose an alternative mechanism in which the amino terminus of the chemokine initially forms interactions with the extracellular loops and transmembrane pocket of the receptor, which is followed by the receptor amino terminus wrapping around the core of the chemokine to prolong its residence time. These data provide insight into how ACKR3 competes and cooperates with canonical GPCRs in its function as a scavenger receptor.


Asunto(s)
Quimiocina CXCL12/metabolismo , Quimiocinas/metabolismo , Receptores CXCR/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Secuencia de Aminoácidos , Sitios de Unión/genética , Quimiocina CXCL12/química , Quimiocina CXCL12/genética , Quimiocinas/química , Quimiocinas/genética , Células HEK293 , Humanos , Cinética , Ligandos , Unión Proteica , Dominios Proteicos , Receptores CXCR/química , Receptores CXCR/genética , Receptores CXCR3/química , Receptores CXCR3/genética , Receptores CXCR3/metabolismo , Receptores CXCR4/química , Receptores CXCR4/genética , Receptores CXCR4/metabolismo , Receptores Acoplados a Proteínas G/química , Receptores Acoplados a Proteínas G/genética , Homología de Secuencia de Aminoácido , Transducción de Señal , beta-Arrestinas/química , beta-Arrestinas/genética , beta-Arrestinas/metabolismo
16.
J Biotechnol ; 305: 43-50, 2019 Nov 10.
Artículo en Inglés | MEDLINE | ID: mdl-31505217

RESUMEN

In metabolic engineering and synthetic biology, the number of genes expressed to achieve better production and pathway regulation in each strain is steadily increasing. The method of choice for expression in Escherichia coli is usually one or several multi-copy plasmids. Meanwhile, the industry standard for long-term, robust production is chromosomal integration of the desired genes. Despite recent advances, genetic manipulation of the bacterial chromosome remains more time consuming than plasmid construction. To allow screening of different metabolic engineering strategies at a level closer to industry while maintaining the molecular-biology advantages of plasmid-based expression, we have investigated the single-copy bacterial artificial chromosome (BAC) as a development tool for metabolic engineering. Using (R)-3-hydroxybutyrate as a model product, we show that BAC can outperform multi-copy plasmids in terms of yield, productivity and specific growth rate, with respective increases of 12%, 18%, and 5%. We both show that gene expression by the BAC simplifies pathway optimization and that the phenotype of pathway expression from BAC is very close to that of chromosomal expression. From these results, we conclude that the BAC can provide a simple platform for performing pathway design and optimization.


Asunto(s)
Cromosomas Artificiales Bacterianos/genética , Escherichia coli/genética , Ingeniería Metabólica/métodos , Cromosomas Artificiales Bacterianos/metabolismo , Escherichia coli/metabolismo , Hidroxibutiratos/metabolismo , Plásmidos/genética , Plásmidos/metabolismo , Biología Sintética
17.
Appl Microbiol Biotechnol ; 103(14): 5627-5639, 2019 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-31104101

RESUMEN

Accumulation of acetate is a limiting factor in recombinant production of (R)-3-hydroxybutyrate (3HB) by Escherichia coli in high-cell-density processes. To alleviate this limitation, this study investigated two approaches: (i) deletion of phosphotransacetylase (pta), pyruvate oxidase (poxB), and/or the isocitrate lyase regulator (iclR), known to decrease acetate formation, on bioreactor cultivations designed to achieve high 3HB concentrations. (ii) Screening of different E. coli strain backgrounds (B, BL21, W, BW25113, MG1655, W3110, and AF1000) for their potential as low acetate-forming, 3HB-producing platforms. Deletion of pta and pta-poxB in the AF1000 strain background was to some extent successful in decreasing acetate formation, but also dramatically increased excretion of pyruvate and did not result in increased 3HB production in high-cell-density fed-batch cultivations. Screening of the different E. coli strains confirmed BL21 as a low acetate-forming background. Despite low 3HB titers in low-cell-density screening, 3HB-producing BL21 produced five times less acetic acid per mole of 3HB, which translated into a 2.3-fold increase in the final 3HB titer and a 3-fold higher volumetric 3HB productivity over 3HB-producing AF1000 strains in nitrogen-limited fed-batch cultivations. Consequently, the BL21 strain achieved the hitherto highest described volumetric productivity of 3HB (1.52 g L-1 h-1) and the highest 3HB concentration (16.3 g L-1) achieved by recombinant E. coli. Screening solely for 3HB titers in low-cell-density batch cultivations would not have identified the potential of this strain, reaffirming the importance of screening with the final production conditions in mind.


Asunto(s)
Ácido 3-Hidroxibutírico/biosíntesis , Técnicas de Cultivo Celular por Lotes , Escherichia coli/genética , Escherichia coli/metabolismo , Ingeniería Metabólica , Reactores Biológicos , Proteínas de Escherichia coli/genética , Eliminación de Gen , Ácido Pirúvico
18.
Appl Microbiol Biotechnol ; 103(9): 3693-3704, 2019 May.
Artículo en Inglés | MEDLINE | ID: mdl-30834961

RESUMEN

Biotechnologically produced (R)-3-hydroxybutyrate is an interesting pre-cursor for antibiotics, vitamins, and other molecules benefitting from enantioselective production. An often-employed pathway for (R)-3-hydroxybutyrate production in recombinant E. coli consists of three-steps: (1) condensation of two acetyl-CoA molecules to acetoacetyl-CoA, (2) reduction of acetoacetyl-CoA to (R)-3-hydroxybutyrate-CoA, and (3) hydrolysis of (R)-3-hydroxybutyrate-CoA to (R)-3-hydroxybutyrate by thioesterase. Whereas for the first two steps, many proven heterologous candidate genes exist, the role of either endogenous or heterologous thioesterases is less defined. This study investigates the contribution of four native thioesterases (TesA, TesB, YciA, and FadM) to (R)-3-hydroxybutyrate production by engineered E. coli AF1000 containing a thiolase and reductase from Halomonas boliviensis. Deletion of yciA decreased the (R)-3-hydroxybutyrate yield by 43%, whereas deletion of tesB and fadM resulted in only minor decreases. Overexpression of yciA resulted in doubling of (R)-3-hydroxybutyrate titer, productivity, and yield in batch cultures. Together with overexpression of glucose-6-phosphate dehydrogenase, this resulted in a 2.7-fold increase in the final (R)-3-hydroxybutyrate concentration in batch cultivations and in a final (R)-3-hydroxybutyrate titer of 14.3 g L-1 in fed-batch cultures. The positive impact of yciA overexpression in this study, which is opposite to previous results where thioesterase was preceded by enzymes originating from different hosts or where (S)-3-hydroxybutyryl-CoA was the substrate, shows the importance of evaluating thioesterases within a specific pathway and in strains and cultivation conditions able to achieve significant product titers. While directly relevant for (R)-3-hydroxybutyrate production, these findings also contribute to pathway improvement or decreased by-product formation for other acyl-CoA-derived products.


Asunto(s)
Ácido 3-Hidroxibutírico/biosíntesis , Acilcoenzima A/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/metabolismo , Palmitoil-CoA Hidrolasa/metabolismo , Tioléster Hidrolasas/genética , Ácido 3-Hidroxibutírico/análisis , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Técnicas de Cultivo Celular por Lotes , Escherichia coli/química , Escherichia coli/genética , Proteínas de Escherichia coli/genética , Halomonas/enzimología , Ingeniería Metabólica , Palmitoil-CoA Hidrolasa/genética , Tioléster Hidrolasas/metabolismo
19.
Methods Cell Biol ; 149: 259-288, 2019.
Artículo en Inglés | MEDLINE | ID: mdl-30616824

RESUMEN

The past decade has witnessed remarkable progress in the determination of G protein-coupled receptor (GPCR) structures, profoundly expanding our understanding of how GPCRs recognize ligands, become activated, and interact with intracellular signaling components. In recent years, numerous studies have used solution nuclear magnetic resonance (NMR) spectroscopy to investigate GPCRs, providing fundamental insights into GPCR conformational changes, allostery, dynamics, and other facets of GPCR function are challenging to study using other structural techniques. Despite these advantages, NMR-based studies of GPCRs are few relative to the number of published structures, due in part to the challenges and limitations of NMR for the characterization of large membrane proteins. Several studies have circumvented these challenges using a variety of isotopic labeling strategies, including side chain derivatization and metabolic incorporation of NMR-active nuclei. In this chapter, we provide an overview of different isotopic labeling strategies and describe an in-depth protocol for the expression, purification, and NMR studies of the chemokine GPCR atypical chemokine receptor 3 (ACKR3) via 13CH3-methionine incorporation. The goal of this chapter is to provide a resource to the GPCR community for those interested in pursuing NMR studies of GPCRs.


Asunto(s)
Isótopos de Carbono/química , Espectroscopía de Resonancia Magnética/métodos , Receptores CXCR/metabolismo , Receptores Acoplados a Proteínas G/metabolismo , Coloración y Etiquetado , Vitamina U/metabolismo , Animales , Línea Celular , Humanos , Soluciones
20.
J Hazard Mater ; 365: 74-80, 2019 03 05.
Artículo en Inglés | MEDLINE | ID: mdl-30412809

RESUMEN

Environmental release and accumulation of pharmaceuticals and personal care products is a global concern in view of increased awareness of ecotoxicological effects. Adsorbent properties make the biopolymer melanin an interesting alternative to remove micropollutants from water. Recently, tyrosinase-surface-displaying Escherichia coli was shown to be an interesting self-replicating production system for melanin-covered cells for batch-wise absorption of the model pharmaceutical chloroquine. This work explores the suitability of these melanin-covered E. coli for the continuous removal of pharmaceuticals from wastewater. A continuous-flow membrane bioreactor containing melanized E. coli cells was used for adsorption of chloroquine from the influent until saturation and subsequent regeneration. At a low loading of cells (10 g/L) and high influent concentration of chloroquine (0.1 mM), chloroquine adsorbed until saturation after 26 ± 2 treated reactor volumes (39 ± 3 L). The average effluent concentration during the first 20 h was 0.0018 mM, corresponding to 98.2% removal. Up to 140 ± 6 mg chloroquine bound per gram of cells following mixed homo- and heterogeneous adsorption kinetics. In situ low-pH regeneration released all chloroquine without apparent capacity loss over three consecutive cycles. This shows the potential of melanized cells for treatment of conventional wastewater or highly concentrated upstream sources such as hospitals or manufacturing sites.


Asunto(s)
Reactores Biológicos , Cloroquina/química , Escherichia coli , Melaninas/química , Eliminación de Residuos Líquidos/métodos , Contaminantes Químicos del Agua/química , Adsorción , Membranas Artificiales
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