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Cunha E, Lagoa D, Faria JP, Liu F, Henry CS, Dias O. TranSyT, an innovative framework for identifying transport systems. Bioinformatics 2023; 39:btad466. [PMID: 37589572 PMCID: PMC10444967 DOI: 10.1093/bioinformatics/btad466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/15/2023] [Accepted: 08/10/2023] [Indexed: 08/18/2023] Open
Abstract
MOTIVATION The importance and rate of development of genome-scale metabolic models have been growing for the last few years, increasing the demand for software solutions that automate several steps of this process. However, since TRIAGE's release, software development for the automatic integration of transport reactions into models has stalled. RESULTS Here, we present the Transport Systems Tracker (TranSyT). Unlike other transport systems annotation software, TranSyT does not rely on manual curation to expand its internal database, which is derived from highly curated records retrieved from the Transporters Classification Database and complemented with information from other data sources. TranSyT compiles information regarding transporter families and proteins, and derives reactions into its internal database, making it available for rapid annotation of complete genomes. All transport reactions have GPR associations and can be exported with identifiers from four different metabolite databases. TranSyT is currently available as a plugin for merlin v4.0 and an app for KBase. AVAILABILITY AND IMPLEMENTATION TranSyT web service: https://transyt.bio.di.uminho.pt/; GitHub for the tool: https://github.com/BioSystemsUM/transyt; GitHub with examples and instructions to run TranSyT: https://github.com/ecunha1996/transyt_paper.
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Affiliation(s)
- Emanuel Cunha
- Centre of Biological Engineering, University of Minho, Braga 4704-553, Portugal
| | - Davide Lagoa
- Centre of Biological Engineering, University of Minho, Braga 4704-553, Portugal
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - José P Faria
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Filipe Liu
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Christopher S Henry
- Computing, Environment, and Life Sciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Oscar Dias
- Centre of Biological Engineering, University of Minho, Braga 4704-553, Portugal
- LABBELS—Associate Laboratory, Braga/Guimarães, Portugal
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2
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Hatton CE, Brotherton DH, Spencer M, Cameron AD. Structure of cytosine transport protein CodB provides insight into nucleobase-cation symporter 1 mechanism. EMBO J 2022; 41:e110527. [PMID: 35775318 PMCID: PMC9379551 DOI: 10.15252/embj.2021110527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 05/01/2022] [Accepted: 05/26/2022] [Indexed: 12/29/2022] Open
Abstract
CodB is a cytosine transporter from the Nucleobase‐Cation‐Symport‐1 (NCS1) transporter family, a member of the widespread LeuT superfamily. Previous experiments with the nosocomial pathogen Pseudomonas aeruginosa have shown CodB as also important for the uptake of 5‐fluorocytosine, which has been suggested as a novel drug to combat antimicrobial resistance by suppressing virulence. Here we solve the crystal structure of CodB from Proteus vulgaris, at 2.4 Å resolution in complex with cytosine. We show that CodB carries out the sodium‐dependent uptake of cytosine and can bind 5‐fluorocytosine. Comparison of the substrate‐bound structures of CodB and the hydantoin transporter Mhp1, the only other NCS1 family member for which the structure is known, highlight the importance of the hydrogen bonds that the substrates make with the main chain at the breakpoint in the discontinuous helix, TM6. In contrast to other LeuT superfamily members, neither CodB nor Mhp1 makes specific interactions with residues on TM1. Comparison of the structures provides insight into the intricate mechanisms of how these proteins transport substrates across the plasma membrane.
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Affiliation(s)
| | | | - Mahalah Spencer
- School of Life Sciences, University of Warwick, Coventry, UK
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3
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Gatchell IT, Huntley RB, Schultes NP, Mourad GS. The guanine-hypoxanthine permease GhxP of Erwinia amylovora facilitates the influx of the toxic guanine derivative 6-thioguanine. J Appl Microbiol 2020; 130:2018-2028. [PMID: 33152175 DOI: 10.1111/jam.14925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/02/2020] [Accepted: 11/02/2020] [Indexed: 01/08/2023]
Abstract
AIM Erwinia amylovora is the causal agent of fire blight, a devastating disease of apples and pears. This study determines whether the E. amylovora guanine-hypoxanthine transporter (EaGhxP) is required for virulence and if it can import the E. amylovora produced toxic analogue 6-thioguanine (6TG) into cells. METHODS AND RESULTS Characterization of EaGhxP in guanine transport deficient Escherichia coli reveals that it can transport guanine, hypoxanthine and the toxic analogues 8-azaguanine (8AG) and 6TG. Similarly, EaGhxP transports 8AG and 6TG into E. amylovora cells. EaGhxP has a high affinity for 6TG with a Ki of 3·7 µmol l-1 . An E. amylovora ⊿ghxP::Camr strain shows resistance to growth on 8AG and 6TG. Although EaGhxP is expressed during active disease propagation, it is not necessary for virulence as determined on immature apple and pear assays. CONCLUSIONS EaGhxP is not required for virulence, but it does import 6TG into E. amylovora cells. SIGNIFICANCE AND IMPACT OF THE STUDY As part of the disease establishment process, E. amylovora synthesizes and exports a toxic guanine derivative 6TG. Our results are counter intuitive and show that EaGhxP, an influx transporter, can move 6TG into cells raising questions regarding the role of 6TG in disease establishment.
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Affiliation(s)
- I T Gatchell
- Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, USA
| | - R B Huntley
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - N P Schultes
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, USA
| | - G S Mourad
- Department of Biology, Purdue University Fort Wayne, Fort Wayne, IN, USA
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Nguyen J, Schein J, Hunt K, Tippmann-Feightner J, Rapp M, Stoffer-Bittner A, Nalam V, Funk A, Schultes N, Mourad G. The Nicotiana sylvestris nucleobase cation symporter 1 retains a dicot solute specificity profile. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.plgene.2020.100226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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5
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Stoffer-Bittner AJ, Alexander CR, Dingman DW, Mourad GS, Schultes NP. Functional characterization of the uracil transporter from honeybee pathogen Paenibacillus larvae. Microb Pathog 2018; 124:305-310. [DOI: 10.1016/j.micpath.2018.08.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/25/2018] [Indexed: 11/30/2022]
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6
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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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7
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Patching SG. Recent developments in nucleobase cation symporter-1 (NCS1) family transport proteins from bacteria, archaea, fungi and plants. J Biosci 2018. [DOI: 10.1007/s12038-018-9780-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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8
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Alexander CR, Dingman DW, Schultes NP, Mourad GS. The solute transport profile of two Aza-guanine transporters from the Honey bee pathogen Paenibacillus larvae. FEMS Microbiol Lett 2018; 365:4828326. [DOI: 10.1093/femsle/fny018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/26/2018] [Indexed: 01/05/2023] Open
Affiliation(s)
- Candace R Alexander
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
| | - Douglas W Dingman
- Department of Entomology, The Connecticut Agricultural Experiment Station, 123 Huntington St, New Haven, CT 06511, USA
| | - Neil P Schultes
- Department of Plant Pathology & Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington St, New Haven, CT 06511, USA
| | - George S Mourad
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
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Sioupouli G, Lambrinidis G, Mikros E, Amillis S, Diallinas G. Cryptic purine transporters inAspergillus nidulansreveal the role of specific residues in the evolution of specificity in the NCS1 family. Mol Microbiol 2016; 103:319-332. [DOI: 10.1111/mmi.13559] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/12/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Georgia Sioupouli
- Department of Biology; National and Kapodistrian University of Athens, Panepistimioupolis; Athens 15784 Greece
| | - George Lambrinidis
- Department of Pharmacy; National and Kapodistrian University of Athens, Panepistimioupolis; Athens 15771 Greece
| | - Emmanuel Mikros
- Department of Pharmacy; National and Kapodistrian University of Athens, Panepistimioupolis; Athens 15771 Greece
| | - Sotiris Amillis
- Department of Biology; National and Kapodistrian University of Athens, Panepistimioupolis; Athens 15784 Greece
| | - George Diallinas
- Department of Biology; National and Kapodistrian University of Athens, Panepistimioupolis; Athens 15784 Greece
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Ma P, Patching SG, Ivanova E, Baldwin JM, Sharples D, Baldwin SA, Henderson PJF. Allantoin transport protein, PucI, from Bacillus subtilis: evolutionary relationships, amplified expression, activity and specificity. MICROBIOLOGY-SGM 2016; 162:823-836. [PMID: 26967546 DOI: 10.1099/mic.0.000266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
This work reports the evolutionary relationships, amplified expression, functional characterization and purification of the putative allantoin transport protein, PucI, from Bacillus subtilis. Sequence alignments and phylogenetic analysis confirmed close evolutionary relationships between PucI and membrane proteins of the nucleobase-cation-symport-1 family of secondary active transporters. These include the sodium-coupled hydantoin transport protein, Mhp1, from Microbacterium liquefaciens, and related proteins from bacteria, fungi and plants. Membrane topology predictions for PucI were consistent with 12 putative transmembrane-spanning α-helices with both N- and C-terminal ends at the cytoplasmic side of the membrane. The pucI gene was cloned into the IPTG-inducible plasmid pTTQ18 upstream from an in-frame hexahistidine tag and conditions determined for optimal amplified expression of the PucI(His6) protein in Escherichia coli to a level of about 5 % in inner membranes. Initial rates of inducible PucI-mediated uptake of 14C-allantoin into energized E. coli whole cells conformed to Michaelis-Menten kinetics with an apparent affinity (Kmapp) of 24 ± 3 μM, therefore confirming that PucI is a medium-affinity transporter of allantoin. Dependence of allantoin transport on sodium was not apparent. Competitive uptake experiments showed that PucI recognizes some additional hydantoin compounds, including hydantoin itself, and to a lesser extent a range of nucleobases and nucleosides. PucI(His6) was solubilized from inner membranes using n-dodecyl-β-d-maltoside and purified. The isolated protein contained a substantial proportion of α-helix secondary structure, consistent with the predictions, and a 3D model was therefore constructed on a template of the Mhp1 structure, which aided localization of the potential ligand binding site in PucI.
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Affiliation(s)
- Pikyee Ma
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Simon G Patching
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Ekaterina Ivanova
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Jocelyn M Baldwin
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - David Sharples
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Stephen A Baldwin
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
| | - Peter J F Henderson
- School of BioMedical Sciences and the Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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11
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Rapp M, Schein J, Hunt KA, Nalam V, Mourad GS, Schultes NP. The solute specificity profiles of nucleobase cation symporter 1 (NCS1) from Zea mays and Setaria viridis illustrate functional flexibility. PROTOPLASMA 2016; 253:611-23. [PMID: 26022088 DOI: 10.1007/s00709-015-0838-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/17/2015] [Indexed: 05/07/2023]
Abstract
The solute specificity profiles (transport and binding) for the nucleobase cation symporter 1 (NCS1) proteins, from the closely related C4 grasses Zea mays and Setaria viridis, differ from that of Arabidopsis thaliana and Chlamydomonas reinhardtii NCS1. Solute specificity profiles for NCS1 from Z. mays (ZmNCS1) and S. viridis (SvNCS1) were determined through heterologous complementation studies in NCS1-deficient Saccharomyces cerevisiae strains. The four Viridiplantae NCS1 proteins transport the purines adenine and guanine, but unlike the dicot and algal NCS1, grass NCS1 proteins fail to transport the pyrimidine uracil. Despite the high level of amino acid sequence similarity, ZmNCS1 and SvNCS1 display distinct solute transport and recognition profiles. SvNCS1 transports adenine, guanine, hypoxanthine, cytosine, and allantoin and competitively binds xanthine and uric acid. ZmNCS1 transports adenine, guanine, and cytosine and competitively binds, 5-fluorocytosine, hypoxanthine, xanthine, and uric acid. The differences in grass NCS1 profiles are due to a limited number of amino acid alterations. These amino acid residues do not correspond to amino acids essential for overall solute and cation binding or solute transport, as previously identified in bacterial and fungal NCS1, but rather may represent residues involved in subtle solute discrimination. The data presented here reveal that within Viridiplantae, NCS1 proteins transport a broad range of nucleobase compounds and that the solute specificity profile varies with species.
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Affiliation(s)
- Micah Rapp
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN, 46805, USA
| | - Jessica Schein
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN, 46805, USA
| | - Kevin A Hunt
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN, 46805, USA
| | - Vamsi Nalam
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN, 46805, USA
| | - George S Mourad
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN, 46805, USA
| | - Neil P Schultes
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington St, New Haven, CT, 06511, USA.
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12
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Minton JA, Rapp M, Stoffer AJ, Schultes NP, Mourad GS. Heterologous complementation studies reveal the solute transport profiles of a two-member nucleobase cation symporter 1 (NCS1) family in Physcomitrella patens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 100:12-17. [PMID: 26773540 DOI: 10.1016/j.plaphy.2015.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/22/2015] [Accepted: 12/23/2015] [Indexed: 06/05/2023]
Abstract
As part of an evolution-function analysis, two nucleobase cation symporter 1 (NCS1) from the moss Physcomitrella patens (PpNCS1A and PpNCS1B) are examined--the first such analysis of nucleobase transporters from early land plants. The solute specificity profiles for the moss NCS1 were determined through heterologous expression, growth and radiolabeled uptake experiments in NCS1-deficient Saccharomyces cerevisiae. Both PpNCS1A and 1B, share the same profiles as high affinity transporters of adenine and transport uracil, guanine, 8-azaguanine, 8-azaadenine, cytosine, 5-fluorocytosine, hypoxanthine, and xanthine. Despite sharing the same solute specificity profile, PpNCS1A and PpNCS1B move nucleobase compounds with different efficiencies. The broad nucleobase transport profile of PpNCS1A and 1B differs from the recently-characterized Viridiplantae NCS1 in breadth, revealing a flexibility in solute interactions with NCS1 across plant evolution.
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Affiliation(s)
- Janet A Minton
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
| | - Micah Rapp
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
| | - Amanda J Stoffer
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA
| | - Neil P Schultes
- Department of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, 123 Huntington St, New Haven, CT 06511, USA
| | - George S Mourad
- Department of Biology, Indiana University-Purdue University Fort Wayne, 2101 East Coliseum Blvd., Fort Wayne, IN 46805, USA.
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13
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Krypotou E, Evangelidis T, Bobonis J, Pittis AA, Gabaldón T, Scazzocchio C, Mikros E, Diallinas G. Origin, diversification and substrate specificity in the family of NCS1/FUR transporters. Mol Microbiol 2015; 96:927-50. [DOI: 10.1111/mmi.12982] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/22/2015] [Indexed: 12/19/2022]
Affiliation(s)
- Emilia Krypotou
- Faculty of Biology; University of Athens; Panepistimioupolis Athens 15784 Greece
| | - Thomas Evangelidis
- Faculty of Pharmacy; University of Athens; Panepistimioupolis Athens 15771 Greece
| | - Jacob Bobonis
- Faculty of Biology; University of Athens; Panepistimioupolis Athens 15784 Greece
| | - Alexandros A. Pittis
- Bioinformatics and Genomics Programme; Centre for Genomic Regulation (CRG); Dr. Aiguader, 88 Barcelona 08003 Spain
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra (UPF); Barcelona 08003 Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme; Centre for Genomic Regulation (CRG); Dr. Aiguader, 88 Barcelona 08003 Spain
- Department of Experimental and Health Sciences; Universitat Pompeu Fabra (UPF); Barcelona 08003 Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA); Pg. Lluís Companys 23 Barcelona 08010 Spain
| | - Claudio Scazzocchio
- Department of Microbiology; Imperial College; London SW7 2AZ UK
- Institut de Génétique et Microbiologie; Université Paris-Sud; France
| | - Emmanuel Mikros
- Faculty of Pharmacy; University of Athens; Panepistimioupolis Athens 15771 Greece
| | - George Diallinas
- Faculty of Biology; University of Athens; Panepistimioupolis Athens 15784 Greece
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Simmons KJ, Jackson SM, Brueckner F, Patching SG, Beckstein O, Ivanova E, Geng T, Weyand S, Drew D, Lanigan J, Sharples DJ, Sansom MSP, Iwata S, Fishwick CWG, Johnson AP, Cameron AD, Henderson PJF. Molecular mechanism of ligand recognition by membrane transport protein, Mhp1. EMBO J 2014; 33:1831-44. [PMID: 24952894 PMCID: PMC4195764 DOI: 10.15252/embj.201387557] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The hydantoin transporter Mhp1 is a sodium-coupled secondary active transport protein of the nucleobase-cation-symport family and a member of the widespread 5-helix inverted repeat superfamily of transporters. The structure of Mhp1 was previously solved in three different conformations providing insight into the molecular basis of the alternating access mechanism. Here, we elucidate detailed events of substrate binding, through a combination of crystallography, molecular dynamics, site-directed mutagenesis, biochemical/biophysical assays, and the design and synthesis of novel ligands. We show precisely where 5-substituted hydantoin substrates bind in an extended configuration at the interface of the bundle and hash domains. They are recognised through hydrogen bonds to the hydantoin moiety and the complementarity of the 5-substituent for a hydrophobic pocket in the protein. Furthermore, we describe a novel structure of an intermediate state of the protein with the external thin gate locked open by an inhibitor, 5-(2-naphthylmethyl)-L-hydantoin, which becomes a substrate when leucine 363 is changed to an alanine. We deduce the molecular events that underlie acquisition and transport of a ligand by Mhp1.
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Affiliation(s)
- Katie J Simmons
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Scott M Jackson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Florian Brueckner
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simon G Patching
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, AZ, USA Department of Biochemistry, University of Oxford, Oxford, UK
| | - Ekaterina Ivanova
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Tian Geng
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Simone Weyand
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - David Drew
- Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK
| | - Joseph Lanigan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - David J Sharples
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Mark S P Sansom
- Department of Biochemistry, University of Oxford, Oxford, UK
| | - So Iwata
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK Rutherford Appleton Laboratory, Research Complex at Harwell, Harwell, Oxford, Didcot, UK
| | - Colin W G Fishwick
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - A Peter Johnson
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
| | - Alexander D Cameron
- Membrane Protein Laboratory, Diamond Light Source Harwell Science and Innovation Campus, Chilton, Didcot, UK Division of Molecular Biosciences, Membrane Protein Crystallography Group Imperial College, London, UK School of Life Sciences, University of Warwick, Coventry, UK
| | - Peter J F Henderson
- School of Biomedical Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK
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15
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Witz S, Panwar P, Schober M, Deppe J, Pasha FA, Lemieux MJ, Möhlmann T. Structure-function relationship of a plant NCS1 member--homology modeling and mutagenesis identified residues critical for substrate specificity of PLUTO, a nucleobase transporter from Arabidopsis. PLoS One 2014; 9:e91343. [PMID: 24621654 PMCID: PMC3951388 DOI: 10.1371/journal.pone.0091343] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/08/2014] [Indexed: 11/18/2022] Open
Abstract
Plastidic uracil salvage is essential for plant growth and development. So far, PLUTO, the plastidic nucleobase transporter from Arabidopsis thaliana is the only known uracil importer at the inner plastidic membrane which represents the permeability barrier of this organelle. We present the first homology model of PLUTO, the sole plant NCS1 member from Arabidopsis based on the crystal structure of the benzyl hydantoin transporter MHP1 from Microbacterium liquefaciens and validated by molecular dynamics simulations. Polar side chains of residues Glu-227 and backbones of Val-145, Gly-147 and Thr-425 are proposed to form the binding site for the three PLUTO substrates uracil, adenine and guanine. Mutational analysis and competition studies identified Glu-227 as an important residue for uracil and to a lesser extent for guanine transport. A differential response in substrate transport was apparent with PLUTO double mutants E227Q G147Q and E227Q T425A, both of which most strongly affected adenine transport, and in V145A G147Q, which markedly affected guanine transport. These differences could be explained by docking studies, showing that uracil and guanine exhibit a similar binding mode whereas adenine binds deep into the catalytic pocket of PLUTO. Furthermore, competition studies confirmed these results. The present study defines the molecular determinants for PLUTO substrate binding and demonstrates key differences in structure-function relations between PLUTO and other NCS1 family members.
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Affiliation(s)
- Sandra Witz
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Pankaj Panwar
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Markus Schober
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Johannes Deppe
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Farhan Ahmad Pasha
- Catalysis Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Kingdom of Saudi Arabia
| | - M. Joanne Lemieux
- Membrane Protein Disease Research Group, Department of Biochemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Torsten Möhlmann
- Department of Plant Physiology, University of Kaiserslautern, Kaiserslautern, Germany
- * E-mail:
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Girke C, Daumann M, Niopek-Witz S, Möhlmann T. Nucleobase and nucleoside transport and integration into plant metabolism. FRONTIERS IN PLANT SCIENCE 2014; 5:443. [PMID: 25250038 PMCID: PMC4158802 DOI: 10.3389/fpls.2014.00443] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 08/18/2014] [Indexed: 05/18/2023]
Abstract
Nucleotide metabolism is an essential process in all living organisms. Besides newly synthesized nucleotides, the recycling (salvage) of partially degraded nucleotides, i.e., nucleosides and nucleobases serves to keep the homeostasis of the nucleotide pool. Both types of metabolites are substrates of at least six families of transport proteins in Arabidopsis thaliana (Arabidopsis) with a total of 49 members. In the last years several members of such transport proteins have been analyzed allowing to present a more detailed picture of nucleoside and nucleobase transport and the physiological function of these processes. Besides functioning in nucleotide metabolism it turned out that individual members of the before named transporters exhibit the capacity to transport a wide range of different substrates including vitamins and phytohormones. The aim of this review is to summarize the current knowledge on nucleobase and nucleoside transport processes in plants and integrate this into nucleotide metabolism in general. Thereby, we will focus on those proteins which have been characterized at the biochemical level.
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Affiliation(s)
| | | | | | - Torsten Möhlmann
- *Correspondence: Torsten Möhlmann, Pflanzenphysiologie, Universität Kaiserslautern, Erwin-Schrödinger-Str., Postfach 3049, D-67653 Kaiserslautern, Germany e-mail:
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