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PubMed2005

Correspondence of function and phylogeny of ABC proteins based on an automated analysis of 20 model protein data sets.

Using our BLAST-based procedure RiPE (Retrieval-induced Phylogeny Environment), which automates the evolutionary analysis of a protein family, we assembled a set of 1138 ABC protein components [adenosine triphosphate (ATP)-binding cassette and transmembrane domain] from the protein data sets of 20 model organisms and subjected them to phylogenetic and functional analysis. For maximum speed, we based the alignment directly on a homology search with a profile of all known human ABC proteins and used neighbor-joining tree estimation. All but 11 sequences from Homo sapiens, Arabidopsis thaliana, Drosophila melanogaster, and Saccharomyces cerevisiae were placed into the correct subtree/subfamily, reproducing published classifications of the individual organisms. By following a simple "function transfer rule", our comparative phylogenetic analysis successfully predicted the known function of human ABC proteins in 19 of 22 cases. Three functional predictions did not correspond, and 10 were novel. Predictions based on BLAST alone were inferior in five cases and superior in two. Bacterial sequences were placed close to the root of most subtrees. This placement coincides with domain architecture, suggesting an early diversification of the ABC family before the kingdoms split apart. Our approach can, in principle, be used to annotate any protein family of any organism included in the study.

ATP-Binding Cassette Transporters↗

PubMed1997

Primary structure of human PMP69, a putative peroxisomal ABC-transporter.

We have cloned the cDNA of a novel human ABC-half-transporter highly similar to peroxisomal ABC-half-transporters such as the adrenoleukodystrophy protein (ALDP) and the peroxisomal protein 70 (PMP70). This 2927-bp cDNA codes for a 606 aminoacid (68.6 kDa) protein that was designated PMP69 (putative peroxisomal membrane protein). PMP69 is ubiquitously expressed. Transcript variants resulting from alternative polyadenylation and splicing events including one that confers an alternative C-terminus have been found. The PMP69 gene is localized on chromosome 14q24.3. ABC-half-transporters require a partner ABC-half-transporter to constitute a functional complex, either as a homodimer or a heterodimer. Defects in the gene coding for ALDP are the cause of adrenoleukodystrophy, a demyelinating disorder of the nervous system with strikingly varying clinical courses. PMP70 was implicated in the pathogenesis of a subgroup of Zellweger syndrome, a heterogenous group of peroxisome assembly disorders. PMP69 might be a heterodimer partner for one of these proteins, thus playing a role in modifying the clinical course of ALD or, alternatively, in peroxisome biogenesis.

ATP-Binding Cassette Transporters↗

PubMed1997

cDNA cloning and mRNA expression of the human adrenoleukodystrophy related protein (ALDRP), a peroxisomal ABC transporter.

We have cloned the cDNA containing the complete coding region of the human adrenoleukodystrophy related (ALDR) gene. The 2220-bp open reading frame encodes a 740-amino-acid polypeptide with a predicted molecular weight of 83.3 kDa. The human ALDR protein displays high similarity (62.8% identical amino acid residues) to the human adrenoleukodystrophy (ALD) gene. Analysis of ALDR expression revealed the presence of ALDR mRNA in a variety of human tissues, predominantly in brain and heart. This expression pattern is different from all other known peroxisomal ABC-transporters. Defects in the ALD gene are the primary cause of adrenoleukodystrophy, a demyelinating disorder of the central nervous system. The ALD protein (ALDP) and the ALDR gene product are peroxisomal membrane proteins belonging to the superfamily of transporters containing an ATP-binding cassette (ABC-transporters). All known peroxisomal ABC-transporters represent only one-half of a functional transporter. They are expected to form dimers either as a homodimer or as a heterodimer. ALDRP is a potential dimerization partner of ALDP or other peroxisomal ABC-transporters. The ALDR gene is a candidate for a modifier gene, accounting for the strikingly varying clinical courses of ALD observed even within a family.

ATP Binding Cassette Transporter, Subfamily D↗

PubMed2001

ABCA6, a novel a subclass ABC transporter.

Here we report the cDNA cloning of a novel member of the ABC A transporter subfamily from human macrophages. The identified coding sequence is of 5.0 kb size and contains an open reading frame which encodes a 1617 amino acid polypeptide. Structurally, the putative ABC transporter protein product consists of two tandemly oriented subunits, each composed of a transmembrane domain followed by a nucleotide binding fold, and thus conforms to the group of full-size ABC transporters. We also demonstrate the existence of an alternative transcript that codes for a 637 amino acid protein variant bearing the features of a truncated half-size transporter. Among the human ABC transporter subfamily A the novel transporter shows highest protein sequence homology with ABCA8 (60%), followed by ABCA2 (32%) and ABCA1 (32%), respectively. In agreement with the proposed classification, the novel transporter was designated ABCA6. The ABCA6 gene is ubiquitously expressed with highest mRNA levels in liver, lung, heart and brain. Analysis of the genomic organization demonstrated that the ABCA6 gene is composed of 38 exons which extend across a region of 62 kb size on chromosome 17q24.2. Based on its structural features and its cholesterol-responsive regulation ABCA6 is potentially involved in macrophage lipid homeostasis.

ATP Binding Cassette Transporter 1↗

PubMed1994

Cloning and expression in Escherichia coli of the gene encoding the Proteus vulgaris chondroitin ABC lyase.

The structural gene encoding chondroitin ABC lyase from Proteus vulgaris was cloned and sequenced. This gene consists of a single open reading frame of 3,063 bp, including a sequence (72 bp) for a possible secretory protein leader peptide, preceded by a Shine-Dalgarno ribosomal binding site. Promoter-like and rho-independent terminator sequences were detected upstream and downstream of the open reading frame, respectively. The G+C content of the coding region was 38.6%. The transcription startpoint was located 41-bp upstream of the initiation codon (ATG). Chondroitin ABC lyase is composed of 997 amino acids, and has a relative molecular mass of 112,635. When the 5.2-kb fragment containing the 1.2-kb upstream from the gene was inserted into pSTV29, and cloned in Escherichia coli, chondroitin ABC lyase was induced in the medium containing chondroitin-6-sulfate as the carbon source. On the other hand, when a 4.2-kb fragment containing only 0.2 kb upstream was inserted into pSTV29(pCHS delta 6), and pCHS delta 6 was introduced into E. coli, the enzyme was constitutively produced, even in medium containing glucose as the carbon source. By immunoblot analysis, the polypeptide synthesized by E. coli cells carrying pCHS delta 6 appeared to be the same as that of the purified chondroitin ABC lyase from P. vulgaris.

Amino Acid Sequence↗

PubMed1997

Protein secretion by gram-negative bacterial ABC exporters.

One of the strategies used by Gram-negative bacteria to secrete proteins across the two membranes which delimit the cells, is sec independent and dedicated to proteins lacking an N-terminal signal peptide. It depends on ABC protein-mediated exporters, which consist of three cell envelope proteins: two inner membrane proteins: an ATPase (the ABC protein), a membrane fusion protein (MFP) and an outer membrane polypeptide. Erwinia chrysanthemi metalloproteinases B and C, and Serratia marcescens hemoprotein HasA are secreted by such homologous pathways and interact with the ABC protein. Interaction between the ABC protein and its substrate has also been evidenced by studies on proteinase and HasA hybrid transporters obtained by combining components from each system. Association between hemoprotein HasA and the three exporter/secretion proteins was demonstrated by affinity chromatography on hemin agarose on which the substrate remained bound with the three secretion proteins. The three component association was ordered and substrate binding was required for the formation of this multiprotein complex.

ATP-Binding Cassette Transporters↗

PubMed2001

Electrodiffusional ATP movement through CFTR and other ABC transporters.

The cystic fibrosis transmembrane conductance regulator (CFTR) is a member of the superfamily of ATP-binding cassette (ABC) transporters, also known as traffic ATPases. Recent studies from our laboratory determined that various members of the ABC family of transport proteins mediate the electrodiffusional movement of the nucleotide ATP. In this report, evidence for the movement of cellular nucleotides by the ABC transporter CFTR and related molecules, including P-glycoproteins (Pgp), is reviewed. The wild-type mdr1 gene product, Pgp, enables the spontaneous release of cellular ATP. However, single amino acid substitutions in both nucleotide-binding sites render a dysfunctional Pgp, whose function can only be reversed by voltage activation. This report includes data indicating that reconstitution of highly purified CFTR from human epithelial origin enables the permeation of both Cl and ATP. The relevance of the ABC domains in ATP transport is also explored, and the hypothesis is forwarded that improper ATP transport by a dysfunctional CFTR is a relevant factor in cystic fibrosis.

ATP-Binding Cassette Transporters↗

PubMed2002

Multifunctionality of plant ABC transporters--more than just detoxifiers.

The ABC-transporter superfamily is one of the largest protein families, and members can be found in bacteria, fungi, plants and animals. The first reports on plant ABC transporters showed that they are implicated in detoxification processes. The recent completion of the genomic sequencing of Arabidopsis thaliana (L.) Heynh. [Arabidopsis Genome Initiative (2000) Nature 408:796-815] showed that Arabidopsis contains more than 100 ABC-type proteins; 53 genes code for so-called full-size transporters, which are large proteins of about 150 kDa consisting of two hydrophobic and two hydrophilic domains. The large number of genes in the MDR/MRP and PDR5-like sub-clusters and the strong sequence homology found in many cases suggest functional redundancy. One reason for the high number of genes can be attributed to the duplication of large segments of Arabidopsis chromosomes. Recent results indicate that the function of this protein family is not restricted to detoxification processes. Plant ABC transporters have been demonstrated to participate in chlorophyll biosynthesis, formation of Fe/S clusters, stomatal movement, and probably ion fluxes; hence they may play a central role in plant growth and developmental processes.

ATP-Binding Cassette Transporters↗

PubMed2003

ABC transporters of the wheat pathogen Mycosphaerella graminicola function as protectants against biotic and xenobiotic toxic compounds.

We have studied the role of five ABC transporter genes (MgAtr to MgAtr5) from the wheat pathogen Mycosphaerella graminicola in multidrug resistance (MDR). Complementation of Saccharomyces cerevisiae mutants with the ABC transporter genes from M. graminicola showed that all the genes tested encode proteins that provide protection against chemically unrelated compounds, indicating that their products function as multidrug transporters with distinct but overlapping substrate specificities. Their substrate range in yeast includes fungicides, plant metabolites, antibiotics, and a mycotoxin derived from Fusarium graminearum (diacetoxyscirpenol). Transformants of M. graminicola in which individual ABC transporter genes were deleted or disrupted did not exhibit clear-cut phenotypes, probably due to the functional redundancy of transporters with overlapping substrate specificity. Independently generated MgAtr5 deletion mutants of M. graminicola showed an increase in sensitivity to the putative wheat defence compound resorcinol and to the grape phytoalexin resveratrol, suggesting a role for this transporter in protecting the fungus against plant defence compounds. Bioassays with antagonistic bacteria indicated that MgAtr2 provides protection against metabolites produced by Pseudomonas fluorescens and Burkholderia cepacia. In summary, our results show that ABC transporters from M. graminicola play a role in protection against toxic compounds of natural and artificial origin.

ATP-Binding Cassette Transporters↗

PubMed2005

ABC proteins: key molecules for lipid homeostasis.

Forty-nine ABC protein genes exist on human chromosomes. Eukaryotic ABC proteins were originally recognized as drug efflux pumps involved in the multidrug resistance of cancer cells. However, it is now realized that one of their major physiological roles is cellular lipid transport and homeostasis, and their dysfunction is often associated with human diseases. ABCA1 and ABCA7 mediate the apolipoprotein-dependent formation of a high-density lipoprotein-cholesterol complex. ABCA3 is indispensable for pulmonary surfactant secretion. ABCG5 and ABCG8 are involved in the secretion of plant sterols and cholesterol into bile. However, the primary substrates and mechanism of action of these ABC proteins have not been precisely defined. In this review article, we first describe the general structure and functions of eukaryotic ABC proteins. The current model of ABCA1 functionality is then explained based on studies on a topological model, subcellular localization, apoA-I dependence of HDL formation, functional defects of Tangier disease mutants, and ATP hydrolysis of purified ABCA1. ABCA1 is supposed to function as a transporter of lipids as well as a receptor for apoA-I. ABCA3 is likely involved in accumulating phospholipids and cholesterol in lamellar bodies and in generating multivesicular structures.

ATP-Binding Cassette Transporters↗

PubMed2006

Heteronuclear multidimensional NMR and homology modelling studies of the C-terminal nucleotide-binding domain of the human mitochondrial ABC transporter ABCB6.

Human ATP-binding cassette, sub-family B, member 6 (ABCB6) is a mitochondrial ABC transporter, and presumably contributes to iron homeostasis. Aimed at understanding the structural basis for the conformational changes accompanying the substrate-transportation cycle, we have studied the C-terminal nucleotide-binding domain of ABCB6 (ABCB6-C) in both the nucleotide-free and ADP-bound states by heteronuclear multidimensional NMR and homology modelling. A non-linear sampling scheme was utilised for indirectly acquired 13C and 15N dimensions of all 3D triple-resonance NMR experiments, in order to overcome the instability and the low solubility of ABCB6-C. The backbone resonances for approximately 25% of non-proline residues, which are mostly distributed around the functionally important loops and in the Helical domain, were not observed for nucleotide-free form of ABCB6-C. From the pH, temperature and magnetic field strength dependencies of the resonance intensities, we concluded that this incompleteness in the assignments is mainly due to the exchange between multiple conformations at an intermediate rate on the NMR timescale. These localised conformational dynamics remained in ADP-bound ABCB6-C except for the loops responsible for adenine base and alpha/beta-phosphate binding. These results revealed that the localised dynamic cooperativity, which was recently proposed for a prokaryotic ABC MJ1267, also exists in a higher eukaryotic ABC, and is presumably shared by all members of the ABC family. Since the Helical domain is the putative interface to the transmembrane domain, this cooperativity may explain the coupled functions between domains in the substrate-transportation cycle.

ATP-Binding Cassette Transporters↗

PubMed1983

The demonstration of terminal deoxynucleotidyl transferase on frozen tissue sections and smears by the avidin-biotin complex (ABC) method.

A method using avidin-biotin complex (ABC) to detect the presence of the enzyme terminal deoxynucleotidyl transferase (TdT) is described and compared with a proven indirect immunofluorescence method. The material studied consisted of: (1) peripheral blood and bone marrow smears from 17 patients with leukemia (ALL, 8; CLL, 3; AML, 6), six normal controls, one T-ALL cell line, and (2) frozen tissue sections from four patients with lymphoblastic lymphoma (LL), two patients with nodular poorly differentiated lymphocytic lymphoma (NLPD), two patients with reactive follicular hyperplasia (RFH) and one calf thymus. The slides from patients with ALL had from 30 to 90% cells with nuclear positively by the ABC technique. Slides from patients with CLL were negative, as were the normal peripheral blood smears. Normal bone marrow smears contained less than 5% positive cells. The T-ALL cell line was 100% positive. The frozen tissue sections from the patients with LL and the calf thymus contained numerous positive cells, while all of the sections from the patients with NLPD and RFH were negative. A good correlation existed between the ABC and the indirect immunofluorescence methods. The ABC method described is both more specific and more sensitive than the previously described techniques in detecting TdT in tissue sections and smear preparations.

Antigens, Surface↗

PubMed1996

Cloning and sequence analysis of a novel member of the ATP-binding cassette (ABC) protein gene family from Plasmodium falciparum.

We have employed oligonucleotide primers directed against the Walker A and B ATP-binding consensus motifs in a PCR-approach to clone a novel member of the eukaryotic ABC protein family of genes from Plasmodium falciparum. The novel gene is predicted to encode a 95.5-kDa protein with two ATP-binding folds each containing a Walker A and B consensus motif and an ABC protein signature sequence. The predicted protein is highly hydrophilic and contains numerous phosphorylation consensus sites but does not contain any potential membrane spanning domains. The gene is present on chromosome 11 and is expressed as a 3.3-kb transcript. The closest homologue with known function to the plasmodial gene is the yeast GCN20 gene which is part of the translation initiation pathway in amino acid starved yeast cells. We have therefore tentatively named the gene Plasmodium falciparum GCN20 homologue (pfgcn20). The pfgcn20 encoded Pfgcn20 protein is also highly homologous to a number of ATP-binding subunits of prokaryotic ABC transporters. We speculate that Pfgcn20 may be an example of a eukaryotic ATP-binding cytosolic subunit of a multipeptide ABC transporter.

ATP-Binding Cassette Transporters↗

PubMed2006

Leishmania amazonensis: metabolic adaptations induced by resistance to an ABC transporter blocker.

We compared growth rate, cell glucose turnover and expression of ATP-binding-cassette (ABC) transporters in Leishmania amazonensis (LTB0016; LTB) versus LTB(160) selected for resistance against the ABC transporter blocker glibenclamide. Additionally, we evaluated the influence of drug-resistance on Leishmania sensitivity against 2-mercaptoacetate and 2-deoxyglucose. Our data demonstrate that (1) LTB(160) and LTB constitutively express ABC transporters for neutral substrates, (2) glibenclamide resistance induces the expression of organic anion ABC transporters, members of the drug resistance associated transporters subfamily, (3) LTB(160) parasites use less glucose as energy substrate and exhibit a slower glucose uptake than LTB cells, and (4) LTB(160) parasites are less sensitive to 2-mercaptoacetate and 2-deoxyglucose than the glibenclamide-sensitive Leishmania LTB. Together these and previous results indicate that the metabolic adaptations expressed in drug-resistant LTB(160) differ from those described for mammalian drug resistant cells and constitute general mechanisms that underlie drug resistance in Leishmania and may be helpful for identifying alternative strategies to circumvent drug resistance in leishmaniasis.

ATP-Binding Cassette Transporters↗

PubMed2006

Identification and characterization of a putative ABC transporter PltHIJKN required for pyoluteorin production in Pseudomonas sp. M18.

A putative ABC (ATP-binding cassette) transport gene cluster pltHIJKN was identified and characterized within a 7.5-kb genome region downstream of the antibiotic pyoluteorin (Plt) biosynthetic gene cluster in Pseudomonas sp. M18, a rhizosphere bacterium which is of ecological importance for controlling plant diseases caused by soil-borne fungal pathogens. The sequence similarity, conserved domains and hydrophobicity profiles strongly suggest that the pltHIJKN gene products are integrated into a typical three-component ABC export system, which consists of the inner membrane ABC transporter PltIJK, the membrane fusion protein PltH and the outer membrane efflux protein PltN. Mutant strains of M18 defective in pltH or pltI did not produce detectable levels of Plt. Overexpression of the entire pltHIJKN gene cluster resulted in a significant increase of Plt production. Heterogenous expression of the pltHIJKN gene cluster gave rise to a significant enhancement of resistance of E. coli DH5alpha to exogenous Plt. These results indicate that PltHIJKN is required for Plt biosynthesis and resistance, which is likely to be mediated by Plt export using the PltHIJKN transport system. Exogenous Plt induced the expression of both the Plt biosynthetic gene cluster and the ABC transport gene cluster pltHIJKN at the transcriptional level, suggesting that Plt biosynthesis and expression of pltHIJKN are coordinately and similarly regulated in Pseudomonas sp. M18.

ATP-Binding Cassette Transporters↗

PubMed2006

Automated brainstem co-registration (ABC) for MRI.

Group data analysis in brainstem neuroimaging is predicated on accurate co-registration of anatomy. As the brainstem is comprised of many functionally heterogeneous nuclei densely situated adjacent to one another, relatively small errors in co-registration can manifest in increased variance or decreased sensitivity (or significance) in detecting activations. We have devised a 2-stage automated, reference mask guided registration technique (Automated Brainstem Co-registration, or ABC) for improved brainstem co-registration. Our approach utilized a brainstem mask dataset to weight an automated co-registration cost function. Our method was validated through measurement of RMS error at 12 manually defined landmarks. These landmarks were also used as guides for a secondary manual co-registration option, intended for outlier individuals that may not adequately co-register with our automated method. Our methodology was tested on 10 healthy human subjects and compared to traditional co-registration techniques (Talairach transform and automated affine transform to the MNI-152 template). We found that ABC had a significantly lower mean RMS error (1.22 +/- 0.39 mm) than Talairach transform (2.88 +/- 1.22 mm, mu +/- sigma) and the global affine (3.26 +/- 0.81 mm) method. Improved accuracy was also found for our manual-landmark-guided option (1.51 +/- 0.43 mm). Visualizing individual brainstem borders demonstrated more consistent and uniform overlap for ABC compared to traditional global co-registration techniques. Improved robustness (lower susceptibility to outliers) was demonstrated with ABC through lower inter-subject RMS error variance compared with traditional co-registration methods. The use of easily available and validated tools (AFNI and FSL) for this method should ease adoption by other investigators interested in brainstem data group analysis.

Adult↗

PubMed2004

Topological analysis of integral membrane constituents of prokaryotic ABC efflux systems.

The ATP binding cassette (ABC) superfamily consists of dozens of families of transport systems, each of which catalyzes uptake or efflux of a specific type of molecule using ATP hydrolysis to energize transport. While all of the ATP hydrolyzing subunits in the superfamily are homologous, a monophyletic origin of the integral membrane constituents is not established. We have identified a subset of these transmembrane proteins that have a basal unit of four transmembrane alpha-helical segments (TMSs) with a large extracytoplasmic domain between TMSs 1 and 2. These homologues were found to exhibit 4, 8 or 10 putative TMSs per polypeptide chain. The two larger topological types exhibit a 4 TMS repeat element resulting from an internal gene duplication event, and the 10 TMS proteins display an extra two putative TMSs between the two repeat units. Rare intragenic deletions in these homologues gave rise to truncated proteins lacking the extracytoplasmic domain, and some phylogenetic clusters of the 4 TMS membrane proteins (but not the 8 or 10 TMS proteins) are fused N-terminal (never C-terminal) to ATP hydrolyzing domains. Bioinformatic analyses lead to the suggestion that in the larger homologues, the second repeat units are more important for function than the first repeat units. Operon analyses suggest that the 4 TMS proteins form heterodimeric complexes while the 8 and 10 TMS proteins incorporate the equivalent of these complexes into single integral membrane polypeptide chains. Different gene compositions of the operons encoding the 4 versus 8 and 10 TMS homologues suggest that these two structural types of transporters act on different types of substrates and serve dissimilar functions. Significant sequence similarity between the integral membrane constituents of the ABC efflux pumps analyzed here and those of other ABC transporters could not be detected. These studies define the evolutionary pathway taken for the appearance of a subset of ABC transmembrane transport proteins and provide clues regarding their mechanistic and functional characteristics.

ATP-Binding Cassette Transporters↗

PubMed2004

Structure and mechanism of ABC transporters.

ATP-binding cassette (ABC) transporters facilitate unidirectional translocation of chemically diverse substrates across cell or organelle membranes. The recently determined crystal structures of the vitamin B(12) importer BtuCD and its cognate binding protein BtuF have revealed critical architectural features that are probably shared by other ABC transporters. For example, the arrangement of the ABC domains and their interface with the membrane-spanning domains are probably conserved, whereas the number of transmembrane helices and their arrangement are not. Two distinct mechanistic schemes for how ABC engines couple ATP hydrolysis to substrate transport have been proposed recently and are being explored.

ATP-Binding Cassette Transporters↗