1
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Tatsaki E, Anagnostopoulou E, Zantza I, Lazou P, Mikros E, Frillingos S. Identification of New Specificity Determinants in Bacterial Purine Nucleobase Transporters based on an Ancestral Sequence Reconstruction Approach. J Mol Biol 2021; 433:167329. [PMID: 34710398 DOI: 10.1016/j.jmb.2021.167329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/28/2022]
Abstract
The relation of sequence with specificity in membrane transporters is challenging to explore. Most relevant studies until now rely on comparisons of present-day homologs. In this work, we study a set of closely related transporters by employing an evolutionary, ancestral-reconstruction approach and reveal unexpected new specificity determinants. We analyze a monophyletic group represented by the xanthine-specific XanQ of Escherichia coli in the Nucleobase-Ascorbate Transporter/Nucleobase-Cation Symporter-2 (NAT/NCS2) family. We reconstructed AncXanQ, the putative common ancestor of this clade, expressed it in E. coli K-12, and found that, in contrast to XanQ, it encodes a high-affinity permease for both xanthine and guanine, which also recognizes adenine, hypoxanthine, and a range of analogs. AncXanQ conserves all binding-site residues of XanQ and differs substantially in only five intramembrane residues outside the binding site. We subjected both homologs to rationally designed mutagenesis and present evidence that these five residues are linked with the specificity change. In particular, we reveal Ser377 of XanQ (Gly in AncXanQ) as a major determinant. Replacement of this Ser with Gly enlarges the specificity of XanQ towards an AncXanQ-phenotype. The ortholog from Neisseria meningitidis retaining Gly at this position is also a xanthine/guanine transporter with extended substrate profile like AncXanQ. Molecular Dynamics shows that the S377G replacement tilts transmembrane helix 12 resulting in rearrangement of Phe376 relative to Phe94 in the XanQ binding pocket. This effect may rationalize the enlarged specificity. On the other hand, the specificity effect of S377G can be masked by G27S or other mutations through epistatic interactions.
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Affiliation(s)
- Ekaterini Tatsaki
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Eleni Anagnostopoulou
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece. https://twitter.com/EleniAnagn
| | - Iliana Zantza
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Athens, Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry, Department of Medicine, School of Health Sciences, University of Ioannina, Ioannina, Greece; Institute of Biosciences, University Research Center of Ioannina, Ioannina, Greece.
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2
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Context-dependent Cryptic Roles of Specific Residues in Substrate Selectivity of the UapA Purine Transporter. J Mol Biol 2021; 433:166814. [PMID: 33497644 DOI: 10.1016/j.jmb.2021.166814] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/29/2020] [Accepted: 01/04/2021] [Indexed: 12/22/2022]
Abstract
Members of the ubiquitous Nucleobase Ascorbate Transporter (NAT) family are H+ or Na+ symporters specific for the cellular uptake of either purines and pyrimidines or L-ascorbic acid. Despite the fact that several bacterial and fungal members have been extensively characterised at a genetic, biochemical or cellular level, and crystal structures of NAT members from Escherichia coli and Aspergillus nidulans have been determined pointing to a mechanism of transport, we have little insight on how substrate selectivity is determined. Here, we present systematic mutational analyses, rational combination of mutations, and novel genetic screens that reveal cryptic context-dependent roles of partially conserved residues in the so-called NAT signature motif in determining the specificity of the UapA transporter of A. nidulans. We show that specific NAT signature motif substitutions, alone and in combinations with each other or with distant mutations in residues known to affect substrate selectivity, lead to novel UapA versions possessing variable transport capacities and specificities for nucleobases. In particular, we show that a UapA version including the quadruple mutation T405S/F406Y/A407S/Q408E in the NAT signature motif (UapA-SYSE) becomes incapable of purine transport, but gains a novel pyrimidine-related profile, which can be further altered to a more promiscuous purine/pyrimidine profile when combined with replacements at distantly located residues, especially at F528. Our results reveal that UapA specificity is genetically highly modifiable and allow us to speculate on how the elevator-type mechanism of transport might account for this flexibility.
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3
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Botou M, Yalelis V, Lazou P, Zantza I, Papakostas K, Charalambous V, Mikros E, Flemetakis E, Frillingos S. Specificity profile of NAT/NCS2 purine transporters in
Sinorhizobium
(
Ensifer
)
meliloti. Mol Microbiol 2020; 114:151-171. [DOI: 10.1111/mmi.14503] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 03/16/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Botou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Vassilis Yalelis
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Panayiota Lazou
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Iliana Zantza
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences National and Kapodistrian University of Athens Athens Greece
| | - Konstantinos Papakostas
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Vassiliki Charalambous
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
| | - Emmanuel Mikros
- Division of Pharmaceutical Chemistry Department of Pharmacy School of Health Sciences National and Kapodistrian University of Athens Athens Greece
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology Department of Biotechnology Agricultural University of Athens Athens Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry Department of Medicine School of Health Sciences University of Ioannina Ioannina Greece
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4
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Yang L, Yang L, Yu H, Liu L, Zhao X, Huang X. Conformational transitions of uracil transporter UraA from Escherichia coli: a molecular simulation study. J Biomol Struct Dyn 2018; 36:3398-3410. [DOI: 10.1080/07391102.2017.1388288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Liu Yang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Lianjuan Yang
- The Fungal Reference Laboratory of Shanghai Dermatology Hospital, Shanghai 200050, China
| | - Hui Yu
- Chemistry Teaching Center, College of Chemistry and Biology, Beihai University, Jilin 132013, People’s Republic of China
| | - Lu Liu
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Xi Zhao
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
| | - Xuri Huang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, People’s Republic of China
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5
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Stoffer‐Bittner AJ, Alexander CR, Dingman DW, Mourad GS, Schultes NP. The solute transport and binding profile of a novel nucleobase cation symporter 2 from the honeybee pathogen Paenibacillus larvae. FEBS Open Bio 2018; 8:1322-1331. [PMID: 30087835 PMCID: PMC6070649 DOI: 10.1002/2211-5463.12488] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 06/22/2018] [Accepted: 06/24/2018] [Indexed: 11/29/2022] Open
Abstract
Here, we report that a novel nucleobase cation symporter 2 encoded in the genome of the honeybee bacterial pathogen Paenibacillus larvae reveals high levels of amino acid sequence similarity to the Escherichia coli and Bacillus subtilis uric acid and xanthine transporters. This transporter is named P. larvae uric acid permease-like protein (PlUacP). Even though PlUacP displays overall amino acid sequence similarities, has common secondary structures, and shares functional motifs and functionally important amino acids with E. coli xanthine and uric acid transporters, these commonalities are insufficient to assign transport function to PlUacP. The solute transport and binding profile of PlUacP was determined by radiolabeled uptake experiments via heterologous expression in nucleobase transporter-deficient Saccharomyces cerevisiae strains. PlUacP transports the purines adenine and guanine and the pyrimidine uracil. Hypoxanthine, xanthine, and cytosine are not transported by PlUacP, but, along with uric acid, bind in a competitive manner. PlUacP has strong affinity for adenine Km 7.04 ± 0.18 μm, and as with other bacterial and plant NCS2 proteins, PlUacP function is inhibited by the proton disruptor carbonyl cyanide m-chlorophenylhydrazone. The solute transport and binding profile identifies PlUacP as a novel nucleobase transporter.
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Affiliation(s)
| | | | - Douglas W. Dingman
- Department of EntomologyThe Connecticut Agricultural Experiment StationNew HavenCTUSA
| | - George S. Mourad
- Department of BiologyIndiana University‐Purdue University Fort WayneINUSA
| | - Neil P. Schultes
- Department of Plant Pathology & EcologyThe Connecticut Agricultural Experiment StationNew HavenCTUSA
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6
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Barraco-Vega M, Romero H, Richero M, Cerdeiras MP, Cecchetto G. Functional characterization of two novel purine transporters from the Basidiomycota Phanerochaete chrysosporium. Gene 2017; 601:1-10. [PMID: 27923672 DOI: 10.1016/j.gene.2016.11.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 11/07/2016] [Accepted: 11/17/2016] [Indexed: 12/24/2022]
Abstract
Purine transporters as substrate entry points in organisms, are involved in a number of cellular processes such as nitrogen source uptake, energy metabolism and synthesis of nucleic acids. In this study, two nucleobase transporter genes (phZ, phU) from Phanerochaete chrysosporium were cloned, identified, and functionally characterized. Our results show that PhZ is a transporter of adenine and hypoxanthine, and a protein belonging to the AzgA-like family, whilst PhU belongs to the NAT/NCS2 family, transporting xanthine and uric acid. No other sequences belonging to these families were detected in P. chrysosporium's genome. Phylogenetic analyses show that AzgA-like sequences form monophyletic groups for each major lineage (Ascomycota, Basidiomycota and Zygomycota). In contrast, Ascomycota and Basidiomycota NAT/NCS2 sequences do not form monophyletic groups and several copies of this protein are distributed across the tree. Expression of phU was significantly downregulated in the presence of a primary source like ammonium, and enhanced if purines were present or if the mycelium was nitrogen starved. phZ was clearly induced by its substrates (hypoxanthine, adenine), very lightly induced by xanthine, suppressed by urea and amino acids and expressed at a basal level when uric acid or ammonium was the nitrogen source or when the mycelium was starved for nitrogen. In order to perform substrate analyses, both P. chrysosporium proteins (PhZ, PhU) were expressed in Aspergillus nidulans. Epifluorescent microscopy showed that under inducing conditions, PhZ-GFP and PhU-GFP were present at the plasma membrane of A. nidulans transformed strains, and were internalized in repressed conditions. Our results suggest that in the white-rot fungus P. chrysosporium, phU has a catabolic role and phZ, (less dependent of the nitrogen source), plays a key role in purine acquisition to provide biosynthetic components. These are the first purine transporters characterized in Basidiomycota.
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Affiliation(s)
- Mariana Barraco-Vega
- Microbiología Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay.
| | - Héctor Romero
- Laboratorio de Organización y Evolución del Genoma, Departamento de Ecología y Evolución, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Mariana Richero
- Microbiología Instituto de Química Biológica, Facultad de Ciencias - Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
| | - María Pía Cerdeiras
- Microbiología Departamento de Biociencias, Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
| | - Gianna Cecchetto
- Microbiología Instituto de Química Biológica, Facultad de Ciencias - Facultad de Química, Universidad de la República, Montevideo 11800, Uruguay
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7
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Dissection of Transporter Function: From Genetics to Structure. Trends Genet 2016; 32:576-590. [DOI: 10.1016/j.tig.2016.06.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 06/20/2016] [Accepted: 06/21/2016] [Indexed: 12/20/2022]
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8
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Karena E, Tatsaki E, Lambrinidis G, Mikros E, Frillingos S. Analysis of conserved NCS2 motifs in theEscherichia colixanthine permease XanQ. Mol Microbiol 2015; 98:502-17. [DOI: 10.1111/mmi.13138] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Ekaterini Karena
- Laboratory of Biological Chemistry; University of Ioannina School of Health Sciences; Ioannina Greece
| | - Ekaterini Tatsaki
- Laboratory of Biological Chemistry; University of Ioannina School of Health Sciences; Ioannina Greece
| | - George Lambrinidis
- Laboratory of Pharmaceutical Chemistry; National and Kapodistrian University of Athens School of Pharmacy; Athens Greece
| | - Emmanuel Mikros
- Laboratory of Pharmaceutical Chemistry; National and Kapodistrian University of Athens School of Pharmacy; Athens Greece
| | - Stathis Frillingos
- Laboratory of Biological Chemistry; University of Ioannina School of Health Sciences; Ioannina Greece
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9
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Functional characterization of NAT/NCS2 proteins of Aspergillus brasiliensis reveals a genuine xanthine-uric acid transporter and an intrinsically misfolded polypeptide. Fungal Genet Biol 2015; 75:56-63. [PMID: 25639910 DOI: 10.1016/j.fgb.2015.01.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2014] [Revised: 01/04/2015] [Accepted: 01/21/2015] [Indexed: 01/28/2023]
Abstract
The Nucleobase-Ascorbate Transporter (NAT) family includes members in nearly all domains of life. Functionally characterized NAT transporters from bacteria, fungi, plants and mammals are ion-coupled symporters specific for the uptake of purines, pyrimidines and related analogues. The characterized mammalian NATs are specific for the uptake of L-ascorbic acid. In this work we identify in silico a group of fungal putative transporters, named UapD-like proteins, which represent a novel NAT subfamily. To understand the function and specificity of UapD proteins, we cloned and functionally characterized the two Aspergillus brasiliensis NAT members (named AbUapC and AbUapD) by heterologous expression in Aspergillus nidulans. AbUapC represents canonical NATs (UapC or UapA), while AbUapD represents the new subfamily. AbUapC is a high-affinity, high-capacity, H(+)/xanthine-uric acid transporter, which can also recognize other purines with very low affinity. No apparent transport function could be detected for AbUapD. GFP-tagging showed that, unlike AbUapC which is localized in the plasma membrane, AbUapD is ER-retained and degraded in the vacuoles, a characteristic of misfolded proteins. Chimeric UapA/AbUapD molecules are also turned-over in the vacuole, suggesting that UapD includes intrinsic peptidic sequences leading to misfolding. The possible evolutionary implication of such conserved, but inactive proteins is discussed.
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10
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Diallinas G. Understanding transporter specificity and the discrete appearance of channel-like gating domains in transporters. Front Pharmacol 2014; 5:207. [PMID: 25309439 PMCID: PMC4162363 DOI: 10.3389/fphar.2014.00207] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2014] [Accepted: 08/22/2014] [Indexed: 12/12/2022] Open
Abstract
Transporters are ubiquitous proteins mediating the translocation of solutes across cell membranes, a biological process involved in nutrition, signaling, neurotransmission, cell communication and drug uptake or efflux. Similarly to enzymes, most transporters have a single substrate binding-site and thus their activity follows Michaelis-Menten kinetics. Substrate binding elicits a series of structural changes, which produce a transporter conformer open toward the side opposite to the one from where the substrate was originally bound. This mechanism, involving alternate outward- and inward-facing transporter conformers, has gained significant support from structural, genetic, biochemical and biophysical approaches. Most transporters are specific for a given substrate or a group of substrates with similar chemical structure, but substrate specificity and/or affinity can vary dramatically, even among members of a transporter family that show high overall amino acid sequence and structural similarity. The current view is that transporter substrate affinity or specificity is determined by a small number of interactions a given solute can make within a specific binding site. However, genetic, biochemical and in silico modeling studies with the purine transporter UapA of the filamentous ascomycete Aspergillus nidulans have challenged this dogma. This review highlights results leading to a novel concept, stating that substrate specificity, but also transport kinetics and transporter turnover, are determined by subtle intramolecular interactions between a major substrate binding site and independent outward- or cytoplasmically-facing gating domains, analogous to those present in channels. This concept is supported by recent structural evidence from several, phylogenetically and functionally distinct transporter families. The significance of this concept is discussed in relationship to the role and potential exploitation of transporters in drug action.
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11
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Papakostas K, Botou M, Frillingos S. Functional identification of the hypoxanthine/guanine transporters YjcD and YgfQ and the adenine transporters PurP and YicO of Escherichia coli K-12. J Biol Chem 2013; 288:36827-40. [PMID: 24214977 DOI: 10.1074/jbc.m113.523340] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The evolutionarily broad family nucleobase-cation symporter-2 (NCS2) encompasses transporters that are conserved in binding site architecture but diverse in substrate selectivity. Putative purine transporters of this family fall into one of two homology clusters: COG2233, represented by well studied xanthine and/or uric acid permeases, and COG2252, consisting of transporters for adenine, guanine, and/or hypoxanthine that remain unknown with respect to structure-function relationships. We analyzed the COG2252 genes of Escherichia coli K-12 with homology modeling, functional overexpression, and mutagenesis and showed that they encode high affinity permeases for the uptake of adenine (PurP and YicO) or guanine and hypoxanthine (YjcD and YgfQ). The two pairs of paralogs differ clearly in their substrate and ligand preferences. Of 25 putative inhibitors tested, PurP and YicO recognize with low micromolar affinity N(6)-benzoyladenine, 2,6-diaminopurine, and purine, whereas YjcD and YgfQ recognize 1-methylguanine, 8-azaguanine, 6-thioguanine, and 6-mercaptopurine and do not recognize any of the PurP ligands. Furthermore, the permeases PurP and YjcD were subjected to site-directed mutagenesis at highly conserved sites of transmembrane segments 1, 3, 8, 9, and 10, which have been studied also in COG2233 homologs. Residues irreplaceable for uptake activity or crucial for substrate selectivity were found at positions occupied by similar role amino acids in the Escherichia coli xanthine- and uric acid-transporting homologs (XanQ and UacT, respectively) and predicted to be at or around the binding site. Our results support the contention that the distantly related transporters of COG2233 and COG2252 use topologically similar side chain determinants to dictate their function and the distinct purine selectivity profiles.
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Affiliation(s)
- Konstantinos Papakostas
- From the Laboratory of Biological Chemistry, University of Ioannina Medical School, 45110 Ioannina, Greece
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12
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Frillingos S. Insights to the evolution of Nucleobase-Ascorbate Transporters (NAT/NCS2 family) from the Cys-scanning analysis of xanthine permease XanQ. INTERNATIONAL JOURNAL OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2012; 3:250-272. [PMID: 23097742 PMCID: PMC3476789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Accepted: 07/02/2012] [Indexed: 06/01/2023]
Abstract
The nucleobase-ascorbate transporter or nucleobase-cation symporter-2 (NAT/NCS2) family is one of the five known families of transporters that use nucleobases as their principal substrates and the only one that is evolutionarily conserved and widespread in all major taxa of organisms. The family is a typical paradigm of a group of related transporters for which conservation in sequence and overall structure correlates with high functional variations between homologs. Strikingly, the human homologs fail to recognize nucleobases or related cytotoxic compounds. This fact allows important biomedical perspectives for translation of structure-function knowledge on this family to the rational design of targeted antimicrobial purine-related drugs. To date, very few homologs have been characterized experimentally in detail and only two, the xanthine permease XanQ and the uric acid/xanthine permease UapA, have been studied extensively with site-directed mutagenesis. Recently, the high-resolution structure of a related homolog, the uracil permease UraA, has been solved for the first time with crystallography. In this review, I summarize current knowledge and emphasize how the systematic Cys-scanning mutagenesis of XanQ, in conjunction with existing biochemical and genetic evidence for UapA and the x-ray structure of UraA, allow insight on the structure-function and evolutionary relationships of this important group of transporters. The review is organized in three parts referring to (I) the theory of use of Cys-scanning approaches in the study of membrane transporter families, (II) the state of the art with experimental knowledge and current research on the NAT/NCS2 family, (III) the perspectives derived from the Cys-scanning analysis of XanQ.
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Affiliation(s)
- Stathis Frillingos
- Laboratory of Biological Chemistry, University of Ioannina Medical School 45110 Ioannina Greece
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13
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Kosti V, Lambrinidis G, Myrianthopoulos V, Diallinas G, Mikros E. Identification of the substrate recognition and transport pathway in a eukaryotic member of the nucleobase-ascorbate transporter (NAT) family. PLoS One 2012; 7:e41939. [PMID: 22848666 PMCID: PMC3405029 DOI: 10.1371/journal.pone.0041939] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Accepted: 06/28/2012] [Indexed: 01/08/2023] Open
Abstract
Using the crystal structure of the uracil transporter UraA of Escherichia coli, we constructed a 3D model of the Aspergillus nidulans uric acid-xanthine/H(+) symporter UapA, which is a prototype member of the Nucleobase-Ascorbate Transporter (NAT) family. The model consists of 14 transmembrane segments (TMSs) divided into a core and a gate domain, the later being distinctly different from that of UraA. By implementing Molecular Mechanics (MM) simulations and quantitative structure-activity relationship (SAR) approaches, we propose a model for the xanthine-UapA complex where the substrate binding site is formed by the polar side chains of residues E356 (TMS8) and Q408 (TMS10) and the backbones of A407 (TMS10) and F155 (TMS3). In addition, our model shows several polar interactions between TMS1-TMS10, TMS1-TMS3, TMS8-TMS10, which seem critical for UapA transport activity. Using extensive docking calculations we identify a cytoplasm-facing substrate trajectory (D360, A363, G411, T416, R417, V463 and A469) connecting the proposed substrate binding site with the cytoplasm, as well as, a possible outward-facing gate leading towards the substrate major binding site. Most importantly, re-evaluation of the plethora of available and analysis of a number of herein constructed UapA mutations strongly supports the UapA structural model. Furthermore, modeling and docking approaches with mammalian NAT homologues provided a molecular rationale on how specificity in this family of carriers might be determined, and further support the importance of selectivity gates acting independently from the major central substrate binding site.
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Affiliation(s)
- Vasiliki Kosti
- Faculty of Biology, University of Athens, Panepistimiopolis, Athens, Greece
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14
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Leung J, Cameron AD, Diallinas G, Byrne B. Stabilizing the heterologously expressed uric acid-xanthine transporter UapA from the lower eukaryote Aspergillus nidulans. Mol Membr Biol 2012; 30:32-42. [PMID: 22694048 DOI: 10.3109/09687688.2012.690572] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Despite detailed genetic and mutagenic analysis and a recent high-resolution structure of a bacterial member of the nucleobase-ascorbate transporter (NAT) family, understanding of the mechanism of action of eukaryotic NATs is limited. Preliminary studies successfully expressed and purified wild-type UapA to high homogeneity; however, the protein was extremely unstable, degrading almost completely after 48 h at 4°C. In an attempt to increase UapA stability we generated a number of single point mutants (E356D, E356Q, N409A, N409D, Q408E and G411V) previously shown to have reduced or no transport activity, but correct targeting to the membrane. The mutant UapA constructs expressed well as GFP fusions in Saccharomyces cerevisiae and exhibited similar fluorescent size exclusion chromatography (FSEC) profiles to the wild-type protein, following solubilization in 1% DDM, LDAO or OM + 1 mM xanthine. In order to assess the relative stabilities of the mutants, solubilized fractions prepared in 1% DDM + 1 mM xanthine were heated at 45°C for 10 min prior to FSEC. The Q408E and G411V mutants gave markedly better profiles than either wild-type or the other mutants. Further FSEC analysis following solubilization of the mutants in 1% NG ± xanthine confirmed that G411V is more stable than the other mutants, but showed that Q408E is unstable under these conditions. G411V and an N-terminally truncated construct G411VΔ1-11 were submitted to large-scale expression and purification. Long-term stability analysis revealed that G411VΔ1-11 was the most stable construct and the most suited to downstream structural studies.
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Affiliation(s)
- James Leung
- Division of Molecular Biosciences, Department of Life Sciences, Imperial College London, UK
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15
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Papakostas K, Frillingos S. Substrate selectivity of YgfU, a uric acid transporter from Escherichia coli. J Biol Chem 2012; 287:15684-95. [PMID: 22437829 DOI: 10.1074/jbc.m112.355818] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family includes more than 2,000 members, but only 15 have been characterized experimentally. Escherichia coli has 10 members, of which the uracil permease UraA and the xanthine permeases XanQ and XanP are functionally known. Of the remaining members, YgfU is closely related in sequence and genomic locus with XanQ. We analyzed YgfU and showed that it is a proton-gradient dependent, low-affinity (K(m) 0.5 mM), and high-capacity transporter for uric acid. It also shows a low capacity for transport of xanthine at 37 °C but not at 25 °C. Based on the set of positions delineated as important from our previous Cys-scanning analysis of permease XanQ, we subjected YgfU to rationally designed site-directed mutagenesis. The results show that the conserved His-37 (TM1), Glu-270 (TM8), Asp-298 (TM9), and Gln-318 and Asn-319 (TM10) are functionally irreplaceable, and Thr-100 (TM3) is essential for the uric acid selectivity because its replacement with Ala allows efficient uptake of xanthine. The key role of these residues is corroborated by the conservation pattern and homology modeling on the recently described x-ray structure of permease UraA. In addition, site-specific replacements at TM8 (S271A, M274D, V282S) impair expression in the membrane, and V320N (TM10) inactivates the permease, whereas R327G (TM10) or S426N (TM14) reduces the affinity for uric acid (4-fold increased K(m)). Our study shows that comprehensive analysis of structure-function relationships in a newly characterized transporter can be accomplished with relatively few site-directed replacements, based on the knowledge available from Cys-scanning mutagenesis of a prototypic homolog.
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Affiliation(s)
- Konstantinos Papakostas
- Laboratory of Biological Chemistry, University of Ioannina Medical School, 45110 Ioannina, Greece
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Karena E, Frillingos S. The role of transmembrane segment TM3 in the xanthine permease XanQ of Escherichia coli. J Biol Chem 2011; 286:39595-605. [PMID: 21917919 DOI: 10.1074/jbc.m111.299164] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The xanthine permease XanQ of Escherichia coli is used as a study prototype for function-structure analysis of the ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family. Our previous mutagenesis study of polar residues of XanQ has shown that Asn-93 at the middle of putative TM3 is a determinant of substrate affinity and specificity. To study the role of TM3 in detail we employed Cys-scanning mutagenesis. Using a functional mutant devoid of Cys residues (C-less), each amino acid residue in sequence 79-107 (YGIVGSGLLSIQSVNFSFVTVMIALGSSM) including TM3 (underlined) and flanking sequences was replaced individually with Cys. Of 29 single-Cys mutants, 20 accumulate xanthine to 40-110% of the steady state observed with C-less, six (S88C, F94C, A102C, G104C, S106C) accumulate to low levels (10-30%) and three (G83C, G85C, N93C) are inactive. Extensive mutagenesis reveals that Gly-83 and, to a lesser extent, Gly-85, are crucial for expression in the membrane. Replacements of Asn-93 disrupt affinity (Thr) or permit recognition of 8-methylxanthine which is not a wild-type ligand (Ala, Ser, Asp) and utilization of uric acid which is not a wild-type substrate (Ala, Ser). Replacements of Phe-94 impair affinity for 2-thio and 6-thioxanthine (Tyr) or 3-methylxanthine (Ile). Single-Cys mutants S84C, L86C, L87C, and S95C are highly sensitive to inactivation by N-ethylmaleimide. Our data reveal that key residues of TM3 cluster in two conserved sequence motifs, (83)GSGLL(87) and (93)NFS(95), and highlight the importance of Asn-93 and Phe-94 in substrate recognition and specificity; these findings are supported by structural modeling on the recently described x-ray structure of the uracil-transporting homolog UraA.
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Affiliation(s)
- Ekaterini Karena
- Laboratory of Biological Chemistry, University of Ioannina Medical School, Ioannina, Greece
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Amillis S, Kosti V, Pantazopoulou A, Mikros E, Diallinas G. Mutational Analysis and Modeling Reveal Functionally Critical Residues in Transmembrane Segments 1 and 3 of the UapA Transporter. J Mol Biol 2011; 411:567-80. [DOI: 10.1016/j.jmb.2011.06.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 06/09/2011] [Accepted: 06/14/2011] [Indexed: 11/30/2022]
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Lu F, Li S, Jiang Y, Jiang J, Fan H, Lu G, Deng D, Dang S, Zhang X, Wang J, Yan N. Structure and mechanism of the uracil transporter UraA. Nature 2011; 472:243-6. [PMID: 21423164 DOI: 10.1038/nature09885] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 01/27/2011] [Indexed: 11/09/2022]
Abstract
The nucleobase/ascorbate transporter (NAT) proteins, also known as nucleobase/cation symporter 2 (NCS2) proteins, are responsible for the uptake of nucleobases in all kingdoms of life and for the transport of vitamin C in mammals. Despite functional characterization of the NAT family members in bacteria, fungi and mammals, detailed structural information remains unavailable. Here we report the crystal structure of a representative NAT protein, the Escherichia coli uracil/H(+) symporter UraA, in complex with uracil at a resolution of 2.8 Å. UraA has a novel structural fold, with 14 transmembrane segments (TMs) divided into two inverted repeats. A pair of antiparallel β-strands is located between TM3 and TM10 and has an important role in structural organization and substrate recognition. The structure is spatially arranged into a core domain and a gate domain. Uracil, located at the interface between the two domains, is coordinated mainly by residues from the core domain. Structural analysis suggests that alternating access of the substrate may be achieved through conformational changes of the gate domain.
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Affiliation(s)
- Feiran Lu
- State Key Laboratory of Bio-membrane and Membrane Biotechnology, Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
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Mermelekas G, Georgopoulou E, Kallis A, Botou M, Vlantos V, Frillingos S. Cysteine-scanning analysis of helices TM8, TM9a, and TM9b and intervening loops in the YgfO xanthine permease: a carboxyl group is essential at ASP-276. J Biol Chem 2010; 285:35011-20. [PMID: 20802252 DOI: 10.1074/jbc.m110.170415] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacterial and fungal members of the ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family use the NAT signature motif, a conserved 11-amino acid sequence between amphipathic helices TM9a and TM9b, to define function and selectivity of the purine binding site. To examine the role of flanking helices TM9a, TM9b, and TM8, we employed Cys-scanning analysis of the xanthine-specific homolog YgfO from Escherichia coli. Using a functional mutant devoid of Cys residues (C-less), each amino acid residue in sequences (259)FLVVGTIYLLSVLEAVGDITATAMVSRRPIQGEEYQSRLKGGVLADGLVSVIASAV(314) and (342)TIAVMLVILGLFP(354) including these TMs (underlined) was replaced individually with Cys, except the irreplaceable Glu-272 and Asp-304, which had been studied previously. Of 67 single Cys mutants, 55 accumulate xanthine to 35-140% of the steady state observed with C-less, five (I265C, D276C, I277C, G299C, L350C) accumulate to low levels (10-20%) and seven (T278C, A279C, T280C, A281C, G305C, G351C, P354C) show negligible expression in the membrane. Extensive mutagenesis reveals that a carboxyl group is needed at Asp-276 for high activity and that D276E differs from wild type as it recognizes 8-methylxanthine (K(i) 79 μm) but fails to recognize 2-thioxanthine, 3-methylxanthine or 6-thioxanthine; bulky replacements of Ala-279 or Thr-280 and replacements of Gly-305, Gly-351, or Pro-354 impair activity or expression. Single Cys mutants V261C, A273C, G275C, and S284C are sensitive to inactivation by N-ethylmaleimide and sensitivity of G275C (IC(50) 15 μm) is enhanced in the presence of substrate. The data suggest that residues crucial for the transport mechanism cluster in two conserved motifs, at the cytoplasmic end of TM8 (EXXGDXXAT) and in TM9a (GXXXDG).
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Affiliation(s)
- George Mermelekas
- Laboratory of Biological Chemistry, University of Ioannina Medical School, 45110 Ioannina, Greece
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