Biotin Acceptor Domain Research Articles

Development of a biotinylated broad-specificity single-chain variable fragment antibody and a sensitive immunoassay for detection of organophosphorus pesticides.

Organophosphorus pesticides (OPs) are the most widely used pesticides in agriculture, and OP residues have been broadly reported in food and environmental samples. The aim of this study is to develop a recombinant antibody-based broad-specificity immunoassay for OPs. A phage display library was prepared from a mouse pre-immunized with a generic immunogen of OPs, and a single-chain variable fragment (scFv) antibody was selected. The selected scFv antibody was fused with biotin acceptor domain (BAD) and overexpressed as an inclusion body in Escherichia coli BL21 (DE3). Then, the protein was refolded by stepwise urea gradient dialysis and biotinylated in vitro by E. coli biotin ligase (BirA). Subsequently, the scFv-BAD protein was purified from the biotinylated system with high yield (66.7mgL(-1)) and confirmed by SDS-PAGE and Western blot. Based on the biotinylated scFv-BAD, a sensitive and broad-specificity competitive indirect enzyme-linked immunosorbent assay (ciELISA) for detection of OPs was developed. The cross-reactivity (CR) studies demonstrated that the ciELISA described here exhibited the broadest detection spectrum for OPs up to now, and 30 OPs could be determined with 50% inhibition value (IC50) values ranging from 19.4 to 515.2ngmL(-1). Moreover, the developed ciELISA was used for the recovery study of the spiked samples and showed satisfactory recoveries. Graphical Abstract Schematic diagram of the development of biotinylated broad-specificity single-chain variable fragment antibody-based immunoassay for organophosphorus pesticides.

Real-time monitoring of NKCC2 endocytosis by total internal reflection fluorescence (TIRF) microscopy.

The apical Na-K-2Cl cotransporter (NKCC2) mediates NaCl reabsorption by the thick ascending limb (TAL). The amount of NKCC2 at the apical membrane of TAL cells is determined by exocytic delivery, recycling, and endocytosis. Surface biotinylation allows measurement of NKCC2 endocytosis, but it has low time resolution and does not allow imaging of the dynamic process of endocytosis. We hypothesized that total internal reflection fluorescence (TIRF) microscopy imaging of labeled NKCC2 would allow monitoring of NKCC2 endocytosis in polarized Madin-Darby canine kidney (MDCK) and TAL cells. Thus we generated a NKCC2 construct containing a biotin acceptor domain (BAD) sequence between the transmembrane domains 5 and 6. Once expressed in polarized MDCK or TAL cells, surface NKCC2 was specifically biotinylated by exogenous biotin ligase (BirA). We also demonstrate that expression of a secretory form of BirA in TAL cells induces metabolic biotinylation of NKCC2. Labeling biotinylated surface NKCC2 with fluorescent streptavidin showed that most apical NKCC2 was located within small discrete domains or clusters referred to as "puncta" on the TIRF field. NKCC2 puncta were observed to disappear from the TIRF field, indicating an endocytic event which led to a decrease in the number of surface puncta at a rate of 1.18 ± 0.16%/min in MDCK cells, and a rate 1.09 ± 0.08%/min in TAL cells (n = 5). Treating cells with a cholesterol-chelating agent (methyl-β-cyclodextrin) completely blocked NKCC2 endocytosis. We conclude that TIRF microscopy of labeled NKCC2 allows the dynamic imaging of individual endocytic events at the apical membrane of TAL cells.

Real time monitoring of NKCC2 endocytosis by total internal reflection fluorescence microscopy (892.19)

The apical Na‐K‐2Cl cotransporter NKCC2 mediates NaCl reabsorption by the thick ascending limb (TAL). The amount of NKCC2 at the apical membrane of TALs is determined by dynamic endocytosis from the apical membrane mediated by clathrin and lipid rafts. However, the time resolution of previous methods used to measure endocytosis was low (5 min), and internalization of NKCC2 containing vesicles not measurable. We hypothesize that TIRF microscopy imaging of fluorescently labeled apical NKCC2 would allow us to monitor its endocytosis in real‐time. We transduced polarized MDCK cells (in Transwell filters) with an N‐terminus GFP‐tagged NKCC2 using adenoviruses. Similar to native TALs, GFP‐NKCC2 was located in the apical membrane, at and above tight junctions. Surface biotinylation confirmed targeting of mature GFP‐NKCC2 (≍190 kDa) to the apical membrane. For TIRF imaging, cells were placed in a chamber with the apical membrane facing the TIRF illumination field. To selectively label NKCC2 at the apical surface we generated NKCC2 containing a biotin acceptor domain of 16 aa between one of the extracellular loops. Once expressed in MDCK cells, we specifically biotinylated surface NKCC2 with recombinant biotin ligase. Labeling apical NKCC2 with streptavidin‐Qdot, or streptavidin‐AlexaFluor allowed us to monitor single endocytic events and apical surface NKCC2 distribution in real‐time. In the absence of biotin ligase we did not observe labeling, indicating specificity for NKCC2 labeling. The overall rate of constitutive NKCC2 endocytosis was 1.2±0.1 % per minute (n=6). In MDCK and TAL cells most apical NKCC2 was located within small discrete domains that exhibited little lateral movement. We conclude that TIRF microscopy of labeled NKCC2 allows the imaging of individual endocytic events at the apical membrane.Grant Funding Source: NIH‐AHA

Conformational changes of recombinant Ca2+–ATPase studied by reaction‐induced infrared difference spectroscopy

Recombinant Ca(2+)-ATPase was expressed in Saccharomyces cerevisiae with a biotin-acceptor domain linked to its C-terminus by a thrombin cleavage site. We obtained 200 μg of ~ 70% pure recombinant sarcoendoplasmic reticulum Ca(2+)-ATPase isoform 1a (SERCA1a) from a 6-L yeast culture. The catalytic cycle of SERCA1a was followed in real time using rapid scan FTIR spectroscopy. Different intermediate states (Ca2 E1P and Ca2 E2P) of the recombinant protein were accumulated using different buffer compositions. The difference spectra of their formation from Ca2 E1 had the same spectral features as those from the native rabbit SERCA1a. The enzyme-specific activity for the active enzyme fraction in both samples was also similar. The results show that the recombinant protein obtained from the yeast-based expression system has similar structural and dynamic properties as native rabbit SERCA1a. It is now possible to apply this expression system together with IR spectroscopy to the investigation of the role of individual amino acids.

Single-Particle Tracking of Nav1.6 Demonstrates Different Mechanisms for Sodium Channel Anchoring within the AIS versus the Soma of Hippocampal Neurons

Voltage-gated sodium channels are responsible for the initiation of action potentials in excitable cells. These channels are highly concentrated at the axon initial segment (AIS) of neurons due to their interactions with ankyrin-G. This interaction is mediated by a 9 amino acid sequence, termed the Ankyrin Binding Motif (ABM) present on the II-III linker. In order to study the dynamics of sodium channels in living neurons in real time, we created a fluorescently labeled Nav1.6 protein with an extracellular tag (biotin acceptor domain). We used single-particle tracking of channels labeled with streptavidin conjugated quantum dots (QDs) and/or Alexa594 to directly compare the mobility of Nav1.6 channels localized to the AIS and somatodendritic compartments of 8DIV hippocampal neurons. We observed two populations of Nav1.6 channels, a small mobile population and a much larger immobile population. The mobile channels on the soma had a diffusion coefficient of 0.016 ± 0.008 μm2/s. To determine the role of ankyrin-G binding in the diffusion of the full-length sodium channel, we deleted the ABM from the Nav1.6 construct. As expected, this mutant channel did not concentrate at the AIS and instead was localized throughout the soma and processes, based on both GFP fluorescence and labeling of surface channels using streptavidin conjugated-Alexa594. Single-particle tracking of the mutant channels revealed that the majority of these channels (∼80%) are also immobile in the plasma membrane of the soma and dendrites. This suggests that although binding to ankyrin-G is necessary and sufficient for Nav1.6 to localize to the AIS, a different mechanism is responsible for the localization and membrane dynamics in the somatodendritic region of hippocampal neurons.

Three-Dimensional Localization of the α and β Subunits and of the II-III Loop in the Skeletal Muscle L-type Ca2+ Channel

The L-type Ca(2+) channel (dihydropyridine receptor (DHPR) in skeletal muscle acts as the voltage sensor for excitation-contraction coupling. To better resolve the spatial organization of the DHPR subunits (α(1s) or Ca(V)1.1, α(2), β(1a), δ1, and γ), we created transgenic mice expressing a recombinant β(1a) subunit with YFP and a biotin acceptor domain attached to its N- and C- termini, respectively. DHPR complexes were purified from skeletal muscle, negatively stained, imaged by electron microscopy, and subjected to single-particle image analysis. The resulting 19.1-Å resolution, three-dimensional reconstruction shows a main body of 17 × 11 × 8 nm with five corners along its perimeter. Two protrusions emerge from either face of the main body: the larger one attributed to the α(2)-δ1 subunit that forms a flexible hook-shaped feature and a smaller protrusion on the opposite side that corresponds to the II-III loop of Ca(V)1.1 as revealed by antibody labeling. Novel features discernible in the electron density accommodate the atomic coordinates of a voltage-gated sodium channel and of the β subunit in a single docking possibility that defines the α1-β interaction. The β subunit appears more closely associated to the membrane than expected, which may better account for both its role in localizing the α(1s) subunit to the membrane and its suggested role in excitation-contraction coupling.

Analysis of Voltage-Gated Sodium Channel Membrane Dynamics in Hippocampal Neurons via a Fluorescent Protein and Biotin Tagged Nav1.6 Channel

Voltage-gated sodium channels (Nav) are densely accumulated at the axon initial segment (AIS) of neurons where they are responsible for action potential initiation. The dense clustering of channels at the AIS involves ankyrinG binding, however the details of trafficking these channels to the AIS remains elusive. Furthermore, it is unclear what percentage of AIS channels is actually conducting. Since the large sodium channel cDNAs are difficult to manipulate and suffer from rearrangements in E. coli, the most elegant trafficking work to date has utilized chimeric proteins containing the sodium channel ankyrin-binding motif fused to other membrane proteins. To fully address trafficking in real time, an appropriately tagged full-length and functional channel is required. Therefore, we developed a Nav1.6 tagged with either GFP or Dendra2 fluorescent-proteins on the C-terminus and an extracellular biotin-acceptor-domain (BAD). The BAD allows for visualization and single molecule tracking of quantum-dot-bound sodium channels on the neuronal surface. This modified Nav1.6 demonstrated wild-type activity when expressed in hippocampal neurons. The tagged channel efficiently trafficked to the cell surface and was localized at the AIS as indicated by both confocal and TIRF microscopy. Alexafluor 594-conjugated-streptavidin binding indicated the surface-density of channels at the AIS was approximately 60 times greater than on the soma, comparable to endogenous Nav1.6 channels. Fluorescence recovery after photobleaching (FRAP) and single particle tracking showed that channels at the AIS had recovery time constants of greater than 2 hours and were confined to 60nm +/- 20nm compartments. In summary, we constructed a sodium channel with fluorescent protein and extracellular biotin reporters that has both wild-type trafficking and biophysical properties. This construct will permit the examination of sodium channel turnover, trafficking, diffusion and location-dependent function in neuronal cells.

Use of In Vivo Biotinylation for Chromatin Immunoprecipitation

This unit describes a system for expression of biotinylated proteins in mammalian cells in vivo, and its application to chromatin immunoprecipitation (ChIP). The system is based on co-expression of the target protein fused to a short biotin acceptor domain, together with the biotinylating enzyme BirA from Escherichia coli. The superior strength of the biotin-avidin interaction in the modified ChIP protocol presented here allows one to employ more stringent washing conditions, resulting in a better signal/noise ratio. Methods for interpreting the data obtained from ChIP samples analyzed by qPCR, and methods for testing the efficiency of biotinylation using a streptavidin gel-shift are also presented. In addition, a complementary method, based on isothermal multiple strand displacement amplification (IMDA) of circular concatemers generated from the DNA fragments obtained after ChIP, is described. This method helps to decrease bias in DNA amplification and is useful for the analysis of complex mixtures of DNA fragments typically generated in miniscale ChIP experiments.

Cross-linking of dimeric CitS and GltS transport proteins

CitS of Klebsiella pneumoniae and GltS of Escherichia coli are Na+-dependent secondary transporters from different families that are believed to share the same fold and quaternary structure. A 10 kDa protein tag (Biotin Acceptor Domain [BAD]) was fused to the N-terminus of both proteins (CitS-BAD1 and GltS-BAD1, respectively) and inserted in the central cytoplasmic loop that connects the two halves of the proteins (CitS-BAD260 and GltS-BAD206). Both CitS constructs and GltS-BAD206 were produced and shown to be active transporters, but GltS-BAD1 could not be detected in the membrane. Distance relationships in the complexes were studied by cross-linking studies. Both CitS constructs were shown to be in the dimeric state after purification in detergent by cross-linking with glutaraldehyde. The concentration of glutaraldehyde resulting in 50% cross-linking was significantly higher for CitS-BAD1 than for CitS and CitS-BAD260. Remarkably, GltS and GltS-BAD260 were not cross-linked by glutaraldehyde because of the lack of productive reactive sites. Cross-linking of GltS was observed when the N-terminal 46 residues of CitS with or without BAD at the N-terminus were added to the N-terminus of GltS. The stretch of 46 residues contains the first transmembrane segment of CitS that is missing in the GltS structure. The data support an orientation of the monomers in the dimer with the N-termini close to the dimer interface and the central cytoplasmic loops far away at the ends of the long axis of the dimer structure in a view perpendicular to the membrane.

Turnover and accessibility of a reentrant loop of the Na+-glutamate transporter GltS are modulated by the central cytoplasmic loop

GltS of Escherichia coli is a secondary transporter that catalyzes Na+-glutamate symport. The structural model of GltS shows two homologous domains with inverted membrane topology that are connected by a central loop that resides in the cytoplasm. Each domain contains a reentrant loop structure. Accessibility of the Cys residues in two GltS mutants in which Pro351 and Asn356 in the reentrant loop in the C-terminal domain were replaced by Cys is demonstrated to be sensitive to the catalytic state supporting a role for the reentrant loops in catalysis. Saturating concentrations of the substrate L-glutamate protected both mutants against inactivation by thiol reagents, while the presence of the co-ion Na+ stimulated the inactivation of both mutants. Insertion of the 10 kDa biotin acceptor domain (BAD) of oxaloacetate decarboxylase of Klebsiella pneumoniae in the central cytoplasmic loop blocked the access pathway from the periplasmic side of the membrane to the cysteine residues in mutants P351C and N356C in the reentrant loop. Kinetically, insertion of BAD increased the maximal rate of uptake 2.7-fold while leaving the apparent affinity constants for L-glutamate and Na+ unaltered. The data suggests that insertion of BAD in the central loop results in conformational changes at the translocation site that lower the activation energy of the translocation step without affecting the access pathway from the periplasmic side for substrate and co-ions. It is concluded that changes in the central loop that connects the two domains may have a regulatory function on the activity of the transporter.

3D Structure of a Recombinant DHPR Expressed in Mouse

The dihydropyridine receptor (DHPR) is an L-type Ca2+ channel that acts as the voltage sensor for excitation-contraction coupling in skeletal muscle by tightly controlling the intracellular Ca2+ channel RyR1. Because previous 3D electron microscopic studies have largely not resolved the spatial organization of the DHPR subunits (α1s, α2-δ, β1a, and γ), we constructed mice expressing a β1a subunit with YFP and a biotin acceptor domain attached to its N- and C- termini respectively. This engineered β1a sustains a functional DHPR-RyR1 interaction and viable animals in a β1a null background. DHPRs were purified from mice by means of the (biotinylated) biotin acceptor domain, negatively stained and imaged with electron microscopy. 8,662 individual DHPRs were analyzed using single-particle image processing algorithms. Multivariate statistical analysis, classification, and multi-reference alignment yielded distinct 2D class averages corresponding to different orientations of the macromolecule. The 3D reconstruction, with 25 A resolution, shows two distinct parts: a main body shaped like an irregular pentagon (∼150x125x75 A) with distinct corners, and a hook-shaped feature that extends ∼60 A from the main body. Consistent with the considerable conservation of membrane topology among voltage-gated channels, a good part of the main body can be closely fitted with an atomic structure of a full-length potassium channel, suggesting that the main body contains the α1s subunit. Besides the fitted potassium channel the main body has extra volume that can accommodate the YFP atomic coordinates and other subunits.Supported by NIH/NIAMS (AR055104) to KGB and NIGMS (GM081819) to PDA.

Multimerization domains for antibody phage display and antibody production

High-throughput generation of antibodies for proteome research has become feasible by using antibody gene libraries and in vitro selection methods like phage display. Typically monovalent antibody fragments like scFv, Fab or scFab are obtained by this technology. To mimic the IgG molecule and gain avidity, resulting in stronger binding, multimerization domains can be fused to antibody fragments. Here we systematically analyzed different multimerization domains in respect to three key parameters, crucial for the high-throughput generation of binders. (i) The compatibility to be displayed on phage (assessed for at least three different antibody formats, scFv, Fab and scFab) in combination with five different multimerization domains; (ii) production yields and (iii) oligomerization properties were analyzed for three different scFv fragments. We found that the use of a biotin acceptor domain in combination with an in vivo biotinylation system performed best concerning the key parameters and thus would be a useful tool to generate multimeric antibody complexes on demand from phage display selected antibody fragments with the least effort.

Location of Subunit d in the Peripheral Stalk of the ATP Synthase from Saccharomyces cerevisiae

ATP synthase from Saccharomyces cerevisiae is an approximately 600 kDa membrane protein complex. The enzyme couples the proton motive force across the mitochondrial inner membrane to the synthesis of ATP from ADP and inorganic phosphate. The peripheral stalk subcomplex acts as a stator, preventing the rotation of the soluble F 1 region relative to the membrane-bound F O region during ATP synthesis. Component subunits of the peripheral stalk are Atp5p (OSCP), Atp4p (subunit b), Atp7p (subunit d), and Atp14p (subunit h). X-ray crystallography has defined the structure of a large fragment of the bovine peripheral stalk, including 75% of subunit d (residues 3-123). Docking the peripheral stalk structure into a cryo-EM map of intact yeast ATP synthase showed that residue 123 of subunit d lies close to the bottom edge of F 1. The 37 missing C-terminal residues are predicted to either fold back toward the apex of F 1 or extend toward the membrane. To locate the C terminus of subunit d within the peripheral stalk of ATP synthase from S. cerevisiae, a biotinylation signal was fused to the protein. The biotin acceptor domain became biotinylated in vivo and was subsequently labeled with avidin in vitro. Electron microscopy of the avidin-labeled complex showed the label tethered close to the membrane surface. We propose that the C-terminal region of subunit d spans the gap from F 1 to F O, reinforcing this section of the peripheral stalk.

Avian and 1918 Spanish Influenza A Virus NS1 Proteins Bind to Crk/CrkL Src Homology 3 Domains to Activate Host Cell Signaling

NS1 (nonstructural protein 1) is an important virulence factor of the influenza A virus. We observed that NS1 proteins of the 1918 pandemic virus (A/Brevig Mission/1/18) and many avian influenza A viruses contain a consensus Src homology 3 (SH3) domain-binding motif. Screening of a comprehensive human SH3 phage library revealed the N-terminal SH3 of Crk and CrkL as the preferred binding partners. Studies with recombinant proteins confirmed avid binding of NS1 proteins of the 1918 virus and a representative avian H7N3 strain to Crk/CrkL SH3 but not to other SH3 domains tested, including p85alpha and p85beta. Endogenous CrkL readily co-precipitated NS1 from cells infected with the H7N3 virus. In transfected cells association with CrkL was observed for NS1 of the 1918 and H7N3 viruses but not A/Udorn/72 or A/WSN/33 NS1 lacking this sequence motif. SH3 binding was dispensable for suppression of interferon-induced gene expression by NS1 but was associated with enhanced phosphatidylinositol 3-kinase signaling, as evidenced by increased Akt phosphorylation. Thus, the Spanish Flu virus resembles avian influenza A viruses in its ability to recruit Crk/CrkL to modulate host cell signaling.

Expanding the Substrate Tolerance of Biotin Ligase through Exploration of Enzymes from Diverse Species

Technologies that enable the site-specific conjugation of chemical probes onto proteins are extremely useful for applications in cell biology and proteomics. We cloned, expressed, and purified biotin ligases from nine different species and screened them for the ability to ligate unnatural analogues of biotin onto the human p67 biotin acceptor domain. We discovered that the biotin ligases of Saccharomyces cerevisiae (yeast) and Pyrococcus horikoshii could accept alkyne and azide derivatives of biotin, respectively. HPLC, gel-shift, and mass spectrometry assays confirmed that these ligation reactions were ATP- and enzyme-dependent, as well as site-specific. We used the P. horikoshii-catalyzed azide ligation reaction to site-specifically introduce a phosphine probe onto p67 using the Staudinger ligation. These new ligation reactions demonstrate the differential substrate specificities of biotin ligases from different organisms and open the door to novel protein labeling applications.

Accessibility of Targeted DHPR Sites to Streptavidin and Functional Effects of Binding on EC Coupling

In skeletal muscle, the dihydropyridine receptor (DHPR) in the plasma membrane (PM) serves as a Ca2+ channel and as the voltage sensor for excitation–contraction (EC coupling), triggering Ca2+ release via the type 1 ryanodine receptor (RyR1) in the sarcoplasmic reticulum (SR) membrane. In addition to being functionally linked, these two proteins are also structurally linked to one another, but the identity of these links remains unknown. As an approach to address this issue, we have expressed DHPR α1S or β1a subunits, with a biotin acceptor domain fused to targeted sites, in myotubes null for the corresponding, endogenous DHPR subunit. After saponin permeabilization, the ∼60-kD streptavidin molecule had access to the β1a N and C termini and to the α1S N terminus and proximal II–III loop (residues 671–686). Steptavidin also had access to these sites after injection into living myotubes. However, sites of the α1S C terminus were either inaccessible or conditionally accessible in saponin- permeabilized myotubes, suggesting that these C-terminal regions may exist in conformations that are occluded by other proteins in PM/SR junction (e.g., RyR1). The binding of injected streptavidin to the β1a N or C terminus, or to the α1S N terminus, had no effect on electrically evoked contractions. By contrast, binding of streptavidin to the proximal α1S II–III loop abolished such contractions, without affecting agonist-induced Ca2+ release via RyR1. Moreover, the block of EC coupling did not appear to result from global distortion of the DHPR and supports the hypothesis that conformational changes of the α1S II–III loop are necessary for EC coupling in skeletal muscle.

Metabolic biotinylation of recombinant antibody by biotin ligase retained in the endoplasmic reticulum

Due to its strength and specificity, the interaction between avidin and biotin has been used in a variety of scientific and medical applications ranging from immunohistochemistry to drug targeting. The present study describes two methods for biotinylation of proteins secreted from eukaryotic cells using the Escherichia coli biotin protein ligase. In one system the biotin ligase was co-secreted from the cells along with substrate protein enabling extracellular biotinylation of the tagged protein. In the other system, biotin ligase was engineered to be retained in the endoplasmic reticulum (ER) and metabolically biotinylates the secretory protein as it passes through the ER. An engineered antibody fragment, a diabody with specificity for carcinoembryonic antigen (CEA) was fused to the biotin acceptor domain (123 amino acid) of Propionibacterium shermanii. Coexpression of the fusion protein with ER retained biotin ligase showed higher biotinylation efficiency than biotinylation by co-secreted ligase. Biotinylation of the anti-CEA diabody tagged with a short (15 amino acid, Biotin Avitag™) biotin acceptor peptide was also successful. Utilization of ER retained biotin ligase for biotinylation of protein is an attractive alternative for efficiently producing uniformly biotinylated recombinant proteins for a variety of avidin–biotin technologies.

The proline permease of Aspergillus nidulans: Functional replacement of the native cysteine residues and properties of a cysteine-less transporter

The major proline transporter (PrnB) of Aspergillus nidulans belongs to the Amino acid Polyamine Organocation (APC) transporter superfamily. Members of this family have not been subjected to systematic structure–function relationship studies. In this report, we examine the functional replacement of the three native Cys residues (Cys54, Cys352 and Cys530) of PrnB and the properties of an engineered Cys-less PrnB protein, as background for employing a Cys-scanning mutagenesis approach. We show that simultaneous replacement of Cys54 with Ala, Cys352 with Ala and Cys530 with Ser results in a functional Cys-less PrnB transporter. We also introduce the use of a biotin-acceptor domain tag to quantitate protein levels of the engineered PrnB mutants by Western blot analysis. Finally, by using the background of the Cys-less PrnB transporter, we evaluate the functional importance of amino acids Q219, K245 and F248 of PrnB, which our previous data had suggested to be involved in the mechanism of PrnB-mediated proline uptake. In the current study, we show that K245 and F248 but not Q219 are critical for PrnB-mediated proline uptake.

Expression in yeast and purification of a membrane protein, SERCA1a, using a biotinylated acceptor domain

We have recently described the final steps leading to the crystallization of a mammalian membrane protein, the rabbit sarcoplasmic reticulum Ca 2+-ATPase, after heterologous expression. Here, we detail the initial steps leading to this new purification method. A biotin acceptor domain was fused at the C-terminal part of Ca 2+-ATPase and a thrombin site was inserted between both coding regions. The recombinant protein was expressed under the control of a galactose-inducible promoter in the yeast Saccharomyces cerevisiae. The biotinylation reaction of the protein was performed directly in vivo in yeast. After solubilization of the yeast light membrane fraction, the biotinylated protein was retained specifically using the strong biotin–avidin interaction. Finally, digestion by the protease thrombin allowed the separation of the Ca 2+-ATPase from the biotinylated domain. At this step, Ca 2+-ATPase is in a relatively purified form (about 40%). After a size-exclusion HPLC step, the purity of the protein is about 70%, and evaluation of the conformational changes during the catalytic cycle by monitoring the intrinsic fluorescence is demonstrated. The major advantage of this avidin procedure is the particularly good specific ATPase activity as compared with that of a purified His-tagged Ca 2+-ATPase.

Cloning and functional characterization of two bacterial members of the NAT/NCS2 family inEscherichia coli

The coding potential of the genome of E. coli K-12 includes YgfO and YicE, two members of the evolutionarily conserved NAT/NCS2 transporter family that are highly homologous to each other (45% residue identity) and closely related to UapA of Aspergillus nidulans, a most extensively studied microbial member of this family. YgfO and yicE were cloned from the genome, over-expressed extrachromosomally and assayed for uptake of [(3)H]xanthine and other nucleobases, in E. coli K-12, under conditions of negligible activity of the corresponding endogenous systems. Alternative, essentially equivalent functional versions of YgfO and YicE were engineered by C-terminal tagging with an epitope from the E. coli lactose permease and a biotin-acceptor domain from Klebsiella pneumoniae. Both YgfO and YicE were shown to be present in the plasma membrane of E. coli and function as specific, high-affinity transporters for xanthine (K(m) 4.2-4.6 microM for YgfO, or 2.9-3.8 microM for YicE), in a proton motive force-dependent manner; they display no detectable transport of uracil, hypoxanthine, or uric acid at external concentrations of up to 0.1 mM. Both YgfO and YicE are inefficient in recognizing uric acid or xanthine analogues modified at position 8 of the purine ring (8-methylxanthine, 8-azaxanthine, oxypurinol, allopurinol), which distinguishes them from their fungal homologues UapA and Xut1.