Asymmetric Switching in a Homodimeric ABC Transporter: A Simulation Study

ABC transporters are a large family of membrane proteins involved in a variety of cellular processes, including multidrug and tumor resistance and ion channel regulation. Advances in the structural and functional understanding of ABC transporters have revealed that hydrolysis at the two canonical nucleotide-binding sites (NBSs) is co-operative and non-simultaneous. A conserved core architecture of bacterial and eukaryotic ABC exporters has been established, as exemplified by the crystal structure of the homodimeric multidrug exporter Sav1866. Currently, it is unclear how sequential ATP hydrolysis arises in a symmetric homodimeric transporter, since it implies at least transient asymmetry at the NBSs. We show by molecular dynamics simulation that the initially symmetric structure of Sav1866 readily undergoes asymmetric transitions at its NBSs in a pre-hydrolytic nucleotide configuration. MgATP-binding residues and a network of charged residues at the dimer interface are shown to form a sequence of putative molecular switches that allow ATP hydrolysis only at one NBS. We extend our findings to eukaryotic ABC exporters which often consist of two non-identical half-transporters, frequently with degeneracy substitutions at one of their two NBSs. Interestingly, many residues involved in asymmetric conformational switching in Sav1866 are substituted in degenerate eukaryotic NBS. This finding strengthens recent suggestions that the interplay of a consensus and a degenerate NBS in eukaroytic ABC proteins pre-determines the sequence of hydrolysis at the two NBSs.     

When an ATPase Is Not an ATPase: at Low Temperatures the C-Terminal Domain of the ABC Transporter CvaB Is a GTPase

The ATP-binding cassette (ABC) transporters belong to a large superfamily of proteins which share a common function and a common nucleotide-binding domain. The CvaB protein from Escherichia coli is a member of the bacterial ABC exporter subfamily and is essential for the export of the peptide antibiotic colicin V. Here we report that, surprisingly, the CvaB carboxyl-terminal nucleotide-binding domain (BCTD) can be preferentially cross-linked to GTP but not to ATP at low temperatures. The cross-linking is Mg²⁺ and Mn²⁺ dependent. However, BCTD possesses similar GTPase and ATPase activities at 37°C, with the same kinetic parameters and with similar responses to inhibitors. Moreover, a point mutation (D654H) in CvaB that completely abolishes colicin V secretion severely impairs both GTPase and ATPase activities in the corresponding BCTD, indicating that the two activities are from the same enzyme. Interestingly, hydrolysis activity of ATP is much more cold sensitive than that of GTP: BCTD possesses mainly GTP hydrolysis activity at 10°C, consistent with the cross-linking results. These findings suggest a novel mechanism for an ABC protein-mediated transport with specificity for GTP hydrolysis.     

Generating Symmetry in the Asymmetric ATP-binding Cassette (ABC) Transporter Pdr5 from Saccharomyces cerevisiae

Pdr5 is a plasma membrane-bound ABC transporter from Saccharomyces cerevisiae and is involved in the phenomenon of resistance against xenobiotics, which are clinically relevant in bacteria, fungi, and humans. Many fungal ABC transporters such as Pdr5 display an inherent asymmetry in their nucleotide-binding sites (NBS) unlike most of their human counterparts. This degeneracy of the NBSs is very intriguing and needs explanation in terms of structural and functional relevance. In this study, we mutated nonconsensus amino acid residues in the NBSs to its consensus counterpart and studied its effect on the function of the protein and effect on yeast cells. The completely “regenerated” Pdr5 protein was severely impaired in its function of ATP hydrolysis and of rhodamine 6G transport. Moreover, we observe alternative compensatory mechanisms to counteract drug toxicity in some of the mutants. In essence, we describe here the first attempts to restore complete symmetry in an asymmetric ABC transporter and to study its effects, which might be relevant to the entire class of asymmetric ABC transporters.     

An ABC Transporter Plays a Developmental Aggregation Role in Myxococcus xanthus

Myxococcus xanthus is a gram-negative bacterium which has a complex life cycle. Autochemotaxis, a process whereby cells release a self-generated signaling molecule, may be the principal mechanism facilitating directed motility in both the vegetative swarming and developmental aggregation stages of this life cycle. The process requires the Frz signal transduction system, including FrzZ, a protein which is composed of two domains, both showing homology to the enteric chemotaxis response regulator CheY. The first domain of FrzZ (FrzZ1), when expressed as bait in the yeast two-hybrid system and screened against a library, was shown to potentially interact with the C-terminal portion of a protein encoding an ATP-binding cassette (AbcA). The activation domain-AbcA fusion protein did not interact with the second domain of FrzZ (FrzZ2) or with two other M. xanthus response regulator-containing proteins presented as bait, suggesting that the FrzZ1-AbcA interaction may be specific. Cloning and sequencing of the upstream region of the abcA gene showed the ATP-binding cassette to be linked to a large hydrophobic, potentially membrane-spanning domain. This domain organization is characteristic of a subgroup of ABC transporters which perform export functions. Cloning and sequencing downstream of abcA indicated that the ABC transporter is at the start of an operon containing three open reading frames. An insertion mutation in the abcA gene resulted in cells displaying the frizzy aggregation phenotype, providing additional evidence that FrzZ and AbcA may be part of the same signal transduction pathway. Cells with mutations in genes downstream of abcA showed no developmental defects. Analysis of the proposed exporter role of AbcA in cell mixing experiments showed that the ABC transporter mutant could be rescued by extracellular complementation. We speculate that the AbcA protein may be involved in the export of a molecule required for the autochemotactic process.     

ABC转运蛋白研究的新进展

ABC转运蛋白主要包括P-糖蛋白、多药耐药相关蛋白和乳腺癌耐药蛋白,它们属于同一家族,具有保守的功能结构域和多样化的生物学功能。ABC转运蛋白部分成员的过表达与肿瘤细胞的多药耐药性（MDR）密切相关,是导致化疗失败的主要原因。随着对MDR机制认识的深入,针对多药耐药蛋白的特异结构域已设计出多种形式的MDR逆转药物。近年来发现,ABC转运蛋白广泛存在于多种正常的组织和器官,参与药物和内、外源毒素的吸收、分布和排泄,行使解毒和防御保护的作用。因此,通过转植ABC转运蛋白基因有可能降低经济鱼类、虾等水产品中有毒污染物的积累。     

A Mutation within the Extended X Loop Abolished Substrate-induced ATPase Activity of the Human Liver ATP-binding Cassette (ABC) Transporter MDR3

The human multidrug resistance protein 3 (MDR3/ABCB4) belongs to the ubiquitous family of ATP-binding cassette (ABC) transporters and is located in the canalicular membrane of hepatocytes. There it flops the phospholipids of the phosphatidylcholine (PC) family from the inner to the outer leaflet. Here, we report the characterization of wild type MDR3 and the Q1174E mutant, which was identified previously in a patient with progressive familial intrahepatic cholestasis type 3 (PFIC-3). We expressed different variants of MDR3 in the yeast Pichia pastoris, purified the proteins via tandem affinity chromatography, and determined MDR3-specific ATPase activity in the presence or absence of phospholipids. The ATPase activity of wild type MDR3 was stimulated 2-fold by liver PC or 1,2-dioleoyl-sn-glycero-3-phosphatidylethanolamine lipids. Furthermore, the cross-linking of MDR3 with a thiol-reactive fluorophore blocked ATP hydrolysis and exhibited no PC stimulation. Similarly, phosphatidylethanolamine, phosphatidylserine, and sphingomyelin lipids did not induce an increase of wild type MDR3 ATPase activity. The phosphate analogues beryllium fluoride and aluminum fluoride led to complete inhibition of ATPase activity, whereas orthovanadate inhibited exclusively the PC-stimulated ATPase activity of MDR3. The Q1174E mutation is located in the nucleotide-binding domain in direct proximity of the leucine of the ABC signature motif and extended the X loop, which is found in ABC exporters. Our data on the Q1174E mutant demonstrated basal ATPase activity, but PC lipids were incapable of stimulating ATPase activity highlighting the role of the extended X loop in the cross-talk of the nucleotide-binding domain and the transmembrane domain.     

Energy Coupling Efficiency in the Type I ABC Transporter GlnPQ

Solute transport via ATP binding cassette (ABC) importers involves receptor-mediated substrate binding, which is followed by ATP-driven translocation of the substrate across the membrane. How these steps are exactly initiated and coupled, and how much ATP it takes to complete a full transport cycle, are subject of debate. Here, we reconstitute the ABC importer GlnPQ in nanodiscs and in proteoliposomes and determine substrate-(in)dependent ATP hydrolysis and transmembrane transport. We determined the conformational states of the substrate-binding domains (SBDs) by single-molecule Förster resonance energy transfer measurements. We find that the basal ATPase activity (ATP hydrolysis in the absence of substrate) is mainly caused by the docking of the closed-unliganded state of the SBDs onto the transporter domain of GlnPQ and that, unlike glutamine, arginine binds both SBDs but does not trigger their closing. Furthermore, comparison of the ATPase activity in nanodiscs with glutamine transport in proteoliposomes shows that the stoichiometry of ATP per substrate is close to two. These findings help understand the mechanism of transport and the energy coupling efficiency in ABC transporters with covalently linked SBDs, which may aid our understanding of Type I ABC importers in general.     

Dimer opening of the nucleotide binding domains of ABC transporters after ATP hydrolysis

ABC transporters constitute one of the most abundant membrane transporter families. The most common feature shared in the family is the highly conserved nucleotide binding domains (NBDs) that drive the transport process through binding and hydrolysis of ATP. Molecular dynamics simulations are used to investigate the effect of ATP hydrolysis in the NBDs. Starting with the ATP-bound, closed dimer of MalK, four simulation systems with all possible combinations of ATP or ADP-P_i bound to the two nucleotide binding sites are constructed and simulated with equilibrium molecular dynamics for ∼70 ns each. The results suggest that the closed form of the NBD dimer can only be maintained with two bound ATP molecules; in other words, hydrolysis of one ATP can lead to the opening of the dimer interface of the NBD dimer. Furthermore, we observed that the opening is an immediate effect of hydrolysis of ATP into ADP and P_i rather than the dissociation of hydrolysis products. In addition, the opening is mechanistically triggered by the dissociation of the LSGGQ motif from the bound nucleotide. A metastable ADP-P_i bound conformational state is consistently observed before the dimer opening in all the simulation systems.     

Studies of the ATPase activity of the ABC protein SUR1

The ATP-sensitive potassium (K(ATP)) channel couples glucose metabolism to insulin secretion in pancreatic beta-cells. It comprises regulatory sulfonylurea receptor 1 and pore-forming Kir6.2 subunits. Binding and/or hydrolysis of Mg-nucleotides at the nucleotide-binding domains of sulfonylurea receptor 1 stimulates channel opening and leads to membrane hyperpolarization and inhibition of insulin secretion. We report here the first purification and functional characterization of sulfonylurea receptor 1. We also compared the ATPase activity of sulfonylurea receptor 1 with that of the isolated nucleotide-binding domains (fused to maltose-binding protein to improve solubility). Electron microscopy showed that nucleotide-binding domains purified as ring-like complexes corresponding to approximately 8 momomers. The ATPase activities expressed as maximal turnover rate [in nmol P(i).s(-1).(nmol protein)(-1)] were 0.03, 0.03, 0.13 and 0.08 for sulfonylurea receptor 1, nucleotide-binding domain 1, nucleotide-binding domain 2 and a mixture of nucleotide-binding domain 1 and nucleotide-binding domain 2, respectively. Corresponding K(m) values (in mm) were 0.1, 0.6, 0.65 and 0.56, respectively. Thus sulfonylurea receptor 1 has a lower K(m) than either of the isolated nucleotide-binding domains, and a lower maximal turnover rate than nucleotide-binding domain 2. Similar results were found with GTP, but the K(m) values were lower. Mutation of the Walker A lysine in nucleotide-binding domain 1 (K719A) or nucleotide-binding domain 2 (K1385M) inhibited the ATPase activity of sulfonylurea receptor 1 by 60% and 80%, respectively. Beryllium fluoride (K(i) 16 microm), but not MgADP, inhibited the ATPase activity of sulfonylurea receptor 1. In contrast, both MgADP and beryllium fluoride inhibited the ATPase activity of the nucleotide-binding domains. These data demonstrate that the ATPase activity of sulfonylurea receptor 1 differs from that of the isolated nucleotide-binding domains, suggesting that the transmembrane domains may influence the activity of the protein.     

Structure and Ligand-Binding Properties of the O Antigen ABC Transporter Carbohydrate-Binding Domain

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The ABC Transporter CclEFGH Facilitates the Production of the Circular Bacteriocin Carnocyclin A

Carnocyclin A is a circular bacteriocin produced by Carnobacterium maltaromaticum UAL307. The carnocyclin A gene cluster cclBITCDAEFGH had been previously reported, and it was shown that transformation of C. maltaromaticum UAL26 with cclBITCDA resulted in immunity to, and low production of, carnocyclin A. Here, we demonstrate that full production of carnocyclin A in UAL26 transformants could be achieved when cclBITCDA was complemented with a second plasmid that contains cclEFGH. CclEFGH is a multicomponent ABC transporter that has similarity to As-48EFGH which is involved in the production of enterocin AS-48. Transformation of UAL26 containing cclBITCDA with deletion derivatives of cclEFGH did not increase the production of carnocyclin A, confirming the involvement of CclEFGH in bacteriocin production. Transformants of UAL26 containing cclEFGH showed a slight decrease in sensitivity to carnocyclin A, indicating that CclEFGH might also play a role in immunity.     

An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota

Root exudates influence the surrounding soil microbial community, and recent evidence demonstrates the involvement of ATP-binding cassette (ABC) transporters in root secretion of phytochemicals. In this study, we examined effects of seven Arabidopsis (Arabidopsis thaliana) ABC transporter mutants on the microbial community in native soils. After two generations, only the Arabidopsis abcg30 (Atpdr2) mutant had significantly altered both the fungal and bacterial communities compared with the wild type using automated ribosomal intergenic spacer analysis. Similarly, root exudate profiles differed between the mutants; however, the largest variance from the wild type (Columbia-0) was observed in abcg30, which showed increased phenolics and decreased sugars. In support of this biochemical observation, whole-genome expression analyses of abcg30 roots revealed that some genes involved in biosynthesis and transport of secondary metabolites were up-regulated, while some sugar transporters were down-regulated compared with genome expression in wild-type roots. Microbial taxa associated with Columbia-0 and abcg30 cultured soils determined by pyrosequencing revealed that exudates from abcg30 cultivated a microbial community with a relatively greater abundance of potentially beneficial bacteria (i.e. plant-growth-promoting rhizobacteria and nitrogen fixers) and were specifically enriched in bacteria involved in heavy metal remediation. In summary, we report how a single gene mutation from a functional plant mutant influences the surrounding community of soil organisms, showing that genes are not only important for intrinsic plant physiology but also for the interactions with the surrounding community of organisms as well.The diversity of the microbial (bacterial and fungal) communities in soil is extraordinary; 1 g of soil contains more than 10 billion microorganisms belonging to thousands of different species (Roselló-Mora and Amann, 2001). Soil microbial populations are involved in a framework of interactions known to affect key environmental processes like biogeochemical cycling of nutrients, plant health, and soil quality (Pace, 1997; Barea et al., 2004; Giri et al., 2005). Most of the dynamic soil microbial interactions happen near the plant roots and root soil interface, an area called the rhizosphere (Lynch, 1990; Barea et al., 2002; Bais et al., 2006; Prithiviraj et al., 2007). Rhizosphere microbial communities differ between plant species (Priha et al., 1999; Innes et al., 2004; Batten et al., 2006), between ecotypes/chemotypes within species (Kowalchuk et al., 2006; Micallef et al., 2009), between different developmental stages of a given plant (Mougel et al., 2006; Weisskopf et al., 2006), and from those present in bulk soil (Broz et al., 2007). Different root types can also cultivate specific microbes (Lilijeroth et al., 1991; Yang and Crowley, 2000; Baudoin et al., 2002), a response that has generally been attributed to the microenvironments surrounding a root and the varying ability of specific root types to uptake nutrients from soils and secrete exudates. Recent evidence suggests that specific plant species support a highly coevolved soil fungal community, and this process is mediated by root-secreted compounds (Broeckling et al., 2008). Rhizosphere interactions are initiated by the release of compounds from different organisms, and it is believed that carbon compounds secreted by roots act as substrates for certain species of microbes in the rhizospshere (Morgan et al., 2005).Root exudates are released into the rhizosphere by three major pathways: diffusion, ion channel, and vesicle transport (Bertin et al., 2003). Recent evidence has implicated ATP-binding cassette (ABC) transporters in the secretion of phytochemicals present in the root exudates of Arabidopsis (Arabidopsis thaliana) and other plants (Loyola-Vargas et al., 2007; Sugiyama et al., 2007; Badri et al., 2008; Badri and Vivanco, 2009). ABC transporters are the largest family of membrane transport proteins found in all organisms from bacteria to humans (Higgins, 1992). These transmembrane proteins use the energy of ATP to pump a wide variety of substrates across the membranes, including peptides, carbohydrates, lipids, heavy metal chelates, inorganic acids, steroids, and xenobiotics (Goossens et al., 2003). ABC transporters are also involved in plant disease resistance at the leaf level (Kobae et al., 2006; Stein et al., 2006).There is accumulating evidence that root exudates play a role in establishing specific interactions with particular microbes in the rhizosphere (legume''s symbiotic interaction with rhizobia, interaction of plants with mycorrhizae, and plant-growth-promoting rhizobacteria [PGPR]; Nagahashi and Douds, 2000; Bais et al., 2006, 2008; Prithiviraj et al., 2007; Rudrappa et al., 2008). However, how root exudation processes that result in large-scale changes to the surrounding soil microbial community compared to individual microbes have not been determined, although some recent reviews have referred to it as a biological frontier (O''Connell et al., 1996; Kuiper et al., 2004; Ryan et al., 2009). In contrast, gene deletions and overexpression of specific genes in plants have been shown to attract or deter specific microbes (Widmer, 2007), herbivores, or their predators (Baldwin et al., 2006; Pandey and Baldwin, 2007; Mitra and Baldwin, 2008), and recently it has been shown that mutations in nonpigment floral chemistry genes affect flower visitation by native pollinators (Kessler et al., 2008). Thus, it is possible that gene expression manipulation leading to an altered spectrum of root exudates can influence the widespread community of soil organisms surrounding a plant. Using all available information described above, we present the most comprehensive study on the effect of a single gene mutation in an ABC transporter involved in root secretion of phytochemicals by Arabidopsis on the natural and coevolved soil microbial composition. We further determine the compounds that are likely to have an effect on moderating the microbial composition and characterized specific and natural microbes that interact with Arabidopsis in the soil by employing pyrosequencing technology.