1
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Xu L, Jia W, Tao X, Ye F, Zhang Y, Ding ZJ, Zheng SJ, Qiao S, Su N, Zhang Y, Wu S, Guo J. Structures and mechanisms of the Arabidopsis cytokinin transporter AZG1. Nat Plants 2024; 10:180-191. [PMID: 38172575 DOI: 10.1038/s41477-023-01590-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 11/10/2023] [Indexed: 01/05/2024]
Abstract
Cytokinins are essential for plant growth and development, and their tissue distributions are regulated by transmembrane transport. Recent studies have revealed that members of the 'Aza-Guanine Resistant' (AZG) protein family from Arabidopsis thaliana can mediate cytokinin uptake in roots. Here we present 2.7 to 3.3 Å cryo-electron microscopy structures of Arabidopsis AZG1 in the apo state and in complex with its substrates trans-zeatin (tZ), 6-benzyleaminopurine (6-BAP) or kinetin. AZG1 forms a homodimer and each subunit shares a similar topology and domain arrangement with the proteins of the nucleobase/ascorbate transporter (NAT) family. These structures, along with functional analyses, reveal the molecular basis for cytokinin recognition. Comparison of the AZG1 structures determined in inward-facing conformations and predicted by AlphaFold2 in the occluded conformation allowed us to propose that AZG1 may carry cytokinins across the membrane through an elevator mechanism.
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Affiliation(s)
- Lingyi Xu
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Nanhu Brain-computer Interface Institute, Hangzhou, China.
| | - Wei Jia
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China
- Calibra Lab at DIAN Diagnostics, Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Provinces, Hangzhou, Zhejiang, China
| | - Xin Tao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, China
| | - Fan Ye
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Nanhu Brain-computer Interface Institute, Hangzhou, China
| | - Yan Zhang
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
- Nanhu Brain-computer Interface Institute, Hangzhou, China
| | - Zhong Jie Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shao Jian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shuai Qiao
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Nannan Su
- International Institutes of Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, Zhejiang, China
| | - Yu Zhang
- National Engineering Laboratory of Intelligent Food Technology and Equipment, Zhejiang Key Laboratory for Agro-Food Processing, College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei, China.
| | - Jiangtao Guo
- Department of Biophysics and Department of Neurology of the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Nanhu Brain-computer Interface Institute, Hangzhou, China.
- NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Science and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
- Department of Cardiology, Key Laboratory of Cardiovascular Intervention and Regenerative Medicine of Zhejiang Province, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, Zhejiang, China.
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2
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Wang M, He J, Li S, Cai Q, Zhang K, She J. Structural basis of vitamin C recognition and transport by mammalian SVCT1 transporter. Nat Commun 2023; 14:1361. [PMID: 36914666 PMCID: PMC10011568 DOI: 10.1038/s41467-023-37037-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 03/15/2023] Open
Abstract
Vitamin C (L-ascorbic acid) is an essential nutrient for human health, and its deficiency has long been known to cause scurvy. Sodium-dependent vitamin C transporters (SVCTs) are responsible for vitamin C uptake and tissue distribution in mammals. Here, we present cryogenic electron microscopy structures of mouse SVCT1 in both the apo and substrate-bound states. Mouse SVCT1 forms a homodimer with each protomer containing a core domain and a gate domain. The tightly packed extracellular interfaces between the core domain and gate domain stabilize the protein in an inward-open conformation for both the apo and substrate-bound structures. Vitamin C binds at the core domain of each subunit, and two potential sodium ions are identified near the binding site. The coordination of sodium ions by vitamin C explains their coupling transport. SVCTs probably deliver substrate through an elevator mechanism in combination with local structural arrangements. Altogether, our results reveal the molecular mechanism by which SVCTs recognize vitamin C and lay a foundation for further mechanistic studies on SVCT substrate transport.
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Affiliation(s)
- Mingxing Wang
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China
| | - Jin He
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China
| | - Shanshan Li
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China
| | - Qianwen Cai
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Kaiming Zhang
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China.
| | - Ji She
- MOE Key Laboratory for Cellular Dynamics, Hefei National Research Center for Interdisciplinary Sciences at the Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
- Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, 230026, China.
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3
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Dimakis D, Pyrris Y, Diallinas G. Transmembrane helices 5 and 12 control transport dynamics, substrate affinity, and specificity in the elevator-type UapA transporter. Genetics 2022; 222:6650625. [PMID: 35894659 PMCID: PMC9434233 DOI: 10.1093/genetics/iyac107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/11/2022] [Indexed: 01/17/2023] Open
Abstract
An increasing number of solute transporters have been shown to function with the so-called sliding-elevator mechanism. Despite structural and functional differences, all elevator-type transporters use a common mechanism of substrate translocation via reversible movements of a mobile core domain (the elevator) hosting the substrate binding site along a rigid scaffold domain stably anchored in the plasma membrane via homodimerization. One of the best-studied elevator transporters is the UapA uric acid-xanthine/H+ symporter of the filamentous fungus Aspergillus nidulans. Here, we present a genetic analysis for deciphering the role of transmembrane segments (TMS) 5 and 12 in UapA transport function. We show that specific residues in both TMS5 and TMS12 control, negatively or positively, the dynamics of transport, but also substrate binding affinity and specificity. More specifically, mutations in TMS5 can lead not only to increased rate of transport but also to an inactive transporter due to high-affinity substrate-trapping, whereas mutations in TMS12 lead to apparently uncontrolled sliding and broadened specificity, leading in specific cases to UapA-mediated purine toxicity. Our findings shed new light on how elevator transporters function and how this knowledge can be applied to genetically modify their transport characteristics.
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Affiliation(s)
- Dimitris Dimakis
- Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - Yiannis Pyrris
- Department of Biology, National and Kapodistrian University of Athens, 15784 Athens, Greece
| | - George Diallinas
- Corresponding author: Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784 Athens, Greece.
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4
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Abstract
Elevator-type transporters are a group of proteins translocating nutrients and metabolites across cell membranes. Despite structural and functional differences, elevator-type transporters use a common mechanism of substrate translocation via reversible movements of a mobile core domain (the elevator), which includes the substrate binding site, along a rigid scaffold domain, stably anchored in the plasma membrane. How substrate specificity is determined in elevator transporters remains elusive. Here, I discuss how a recent report on the sliding elevator mechanism, seen under the context of genetic analysis of a prototype fungal transporter, sheds light on how specificity might be genetically modified. I propose that flexible specificity alterations might occur by 'loosening' of the sliding mechanism from tight coupling to substrate binding.
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Affiliation(s)
- George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784, Athens, Greece; Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology, Heraklion, Greece.
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5
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Cecchetti C, Scull NJ, Mohan TC, Alguel Y, Jones AMC, Cameron AD, Byrne B. Transfer of stabilising mutations between different secondary active transporter families. FEBS Open Bio 2021; 11:1685-1694. [PMID: 33932145 PMCID: PMC8167854 DOI: 10.1002/2211-5463.13168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/25/2021] [Accepted: 04/15/2021] [Indexed: 11/24/2022] Open
Abstract
Integral membrane transporters play essential roles in the movement of substrates across biological membranes. One approach to produce transporters suitable for structural studies is to introduce mutations that reduce conformational flexibility and increase stability. However, it can be difficult to predict which mutations will result in a more stable protein. Previously, we stabilised the uric acid‐xanthine transporter, UapA, a member of the SLC23 family, through introduction of a single‐point mutation, G411V, trapping the protein in the inward‐facing conformation. Here, we attempted to stabilise the structurally related BOR1 transporter from Arabidopsis thaliana, a member of the SLC4 family, by introducing the equivalent substitution. We identified possible residues, P362 and M363, in AtBOR1, likely to be equivalent to the G411 of UapA, and generated four mutants, P362V or L and M363F or Y. Stability analysis using heated Fluorescent Size Exclusion Chromatography indicated that the M363F/Y mutants were more stable than the WT AtBOR1 and P362V/L mutants. Furthermore, functional complementation analysis revealed that the M363F/Y mutants exhibited reduced transport activity compared to the P362V/L and WT proteins. Purification and crystallisation of the M363F/Y proteins yielded crystals that diffracted better than WT (5.5 vs 7 Å). We hypothesise that the increased bulk of the F and Y substitutions limits the ability of the protein to undergo the conformational rearrangements associated with transport. These proteins represent a basis for future studies on AtBOR1.
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Affiliation(s)
| | - Nicola J Scull
- Department of Life Sciences, Imperial College London, UK
| | | | - Yilmaz Alguel
- Department of Life Sciences, Imperial College London, UK
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6
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Kourkoulou A, Zantza I, Foti K, Mikros E, Diallinas G. 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] [What about the content of this article? (0)] [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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7
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Chen LY, Zhang LF, Lu ZY, Xian F, Zhang JZ, Cheng YC, Zhang XQ, Liu Y. Effects of Trace Irrigation at Different Depths on Transcriptome Expression Pattern in Cotton ( G. hirsutum L.) Leaves. Biomed Res Int 2020; 2020:7248513. [PMID: 32802872 PMCID: PMC7403946 DOI: 10.1155/2020/7248513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 11/17/2022]
Abstract
Drought is a limiting factor for cotton productivity and quality. Irrigation could increase cotton yield. This study is aimed at formulating a proper irrigation depth for cotton at China' Inner Mongolia and at investigating the molecular mechanism underlying the difference induced by irrigation. Transcriptomic analysis was carried out to reveal the global transcriptome profiles on the leaves of cotton seedlings (G. hirsutum L. cv. "Zhongmian 92") with trace irrigation tapes at 30 cm (D30) and 50 cm (D50) underground. The differentially expressed genes (DEGs) were identified and clustered by functional enrichment analysis. The results showed that no significant differences were found in the lint percentage. The yields of unpinned and lint cotton were increased by the D30 regime but decreased by the D50 regime. Transcriptomic analysis showed that 4,549 nonoverlapped DEGs were identified by comparative analysis. Transcription factors, including bZIP, WARK, Myb, and NAC, were altered between D50 and D30. The D50 regime induced more DEGs compared with the D30 regime, which was associated with plant tolerance to abiotic stresses and drought. In conclusion, trace irrigation at 30 cm underground was suitable for cotton irrigation at China's Inner Mongolia, while the D50 irrigation regime influenced the cotton yield via drought stress in cotton plants.
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Affiliation(s)
- Li-yu Chen
- Hebei Agricultural University, Baoding 071000, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Li-feng Zhang
- Hebei Agricultural University, Baoding 071000, China
| | - Zhan-yuan Lu
- Hebei Agricultural University, Baoding 071000, China
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Feng Xian
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Jian-zhong Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Yu-chen Cheng
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Xiang-qian Zhang
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
| | - Yan Liu
- Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot 010031, China
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8
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Bittner AJ, Huntley RB, Mourad GS, Schultes NP. An Erwinia amylovora uracil transporter mutant retains virulence on immature apple and pear fruit. Microb Pathog 2020; 147:104363. [PMID: 32615243 DOI: 10.1016/j.micpath.2020.104363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/23/2020] [Accepted: 06/24/2020] [Indexed: 12/13/2022]
Abstract
Erwinia amylovora is the causal agent of fire blight, a devastating disease of apples and pears. A previous study revealed that an E. amylovora uracil auxotroph was still virulent and can cause disease, suggesting that uracil can be obtained from the host environment. The E. amylovora genome contains a locus encoding for a uracil transporter belonging to the nucleobase cation symporter 2 family, displaying a high level of amino acid sequence similarity to the Escherichia coli UraA. Expression of E. amylovora UraA in nucleobase transporter-deficient E. coli strains, coupled with radiolabeled uptake studies reveal that E. amylovora UraA is a high affinity uracil transporter with a Km of 0.57 μM. Both E. coli and E. amylovora carrying extra copies of E. amylovora UraA are sensitive to growth on the toxic analog 5-fluorouracil. An E. amylovora ΔuraA::Camr mutant is still able to grow and cause disease symptoms on immature pears and apples.
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9
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Kourkoulou A, Grevias P, Lambrinidis G, Pyle E, Dionysopoulou M, Politis A, Mikros E, Byrne B, Diallinas G. Specific Residues in a Purine Transporter Are Critical for Dimerization, ER Exit, and Function. Genetics 2019; 213:1357-1372. [PMID: 31611232 PMCID: PMC6893392 DOI: 10.1534/genetics.119.302566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/02/2019] [Indexed: 12/11/2022] Open
Abstract
Transporters are transmembrane proteins that mediate the selective translocation of solutes across biological membranes. Recently, we have shown that specific interactions with plasma membrane phospholipids are essential for the formation and/or stability of functional dimers of the purine transporter UapA, a prototypic eukaryotic member of the ubiquitous nucleobase ascorbate transporter (NAT) family. Here, we provide strong evidence that distinct interactions of UapA with membrane lipids are essential for ab initio formation of functional dimers in the ER, or ER exit and further subcellular trafficking. Through genetic screens, we identify mutations that restore defects in dimer formation and/or trafficking. Suppressors of defective dimerization restore ab initio formation of UapA dimers in the ER. Most of these suppressors are located in the movable core domain, but also in the core-dimerization interface and in residues of the dimerization domain exposed to lipids. Molecular dynamics suggest that the majority of suppressors stabilize interhelical interactions in the core domain and thus assist the formation of functional UapA dimers. Among suppressors restoring dimerization, a specific mutation, T401P, was also isolated independently as a suppressor restoring trafficking, suggesting that stabilization of the core domain restores function by sustaining structural defects caused by the abolishment of essential interactions with specific lipids. Importantly, the introduction of mutations topologically equivalent to T401P into a rat homolog of UapA, namely rSNBT1, permitted the functional expression of a mammalian NAT in Aspergillus nidulans Thus, our results provide a potential route for the functional expression and manipulation of mammalian transporters in the model Aspergillus system.
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Affiliation(s)
- Anezia Kourkoulou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784, Greece
| | - Pothos Grevias
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784, Greece
| | - George Lambrinidis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, 15771, Greece
| | - Euan Pyle
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
- Department of Chemistry, King's College London, SE1 1DB, UK
| | - Mariangela Dionysopoulou
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784, Greece
| | | | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis, 15771, Greece
| | - Bernadette Byrne
- Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15784, Greece
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11
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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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 08/25/2018] [Indexed: 11/30/2022]
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Chai W, Peng X, Liu B, Wang J, Zhu Z, Liu Y, Zhao K, Cheng B, Si W, Jiang H. Comparative Genomics, Whole-Genome Re-sequencing and Expression Profile Analysis of Nucleobase:Cation Symporter 2 ( NCS2) Genes in Maize. Front Plant Sci 2018; 9:856. [PMID: 30002663 PMCID: PMC6031955 DOI: 10.3389/fpls.2018.00856] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Accepted: 06/01/2018] [Indexed: 06/08/2023]
Abstract
Nucleobase:cation symporter 2 (NCS2) proteins are important for the transport of free nucleobases, participating in diverse plant growth and developmental processes, as well as response to abiotic stress. To date, a comprehensive analysis of the NCS2 gene family has not been performed in maize. In this study, we conducted a comparative genomics analysis of NCS2 genes in 28 plant species, ranging from aquatic algae to land plants, concentrating mainly on maize. Gene duplication events contributed to the expansion of NCS2 genes from lower aquatic plants to higher angiosperms, and whole-genome/segmental and single-gene duplication events were responsible for the expansion of the maize NCS2 gene family. Phylogenetic construction showed three NCS2 subfamilies, I, II, and III. According to homology-based relationships, members of subfamily I are NCS2/AzgA-like genes, whereas those in subfamilies II and III are NCS2/NATs. Moreover, subfamily I exhibited ancient origins. A motif compositional analysis showed that one symbolic motif (motif 4) of the NCS2/NAT genes was absent in subfamily I. In maize, three NCS2/AzgA-like and 21 NCS2/NAT genes were identified, and purifying selection influenced the duplication of maize NCS2 genes. Additionally, a population genetic analysis of NCS2 genes revealed that ZmNCS2-21 showed the greatest diversity between the 78 inbred and 22 wild surveyed maize populations. An expression profile analysis using transcriptome data and quantitative real-time PCR revealed that NCS2 genes in maize are involved in diverse developmental processes and responses to abiotic stresses, including abscisic acid, salt (NaCl), polyethylene glycol, and low (4°C) and high (42°C) temperatures. ZmNCS2 genes with relatively close relationships had similar expression patterns, strongly indicating functional redundancy. Finally, ZmNCS2-16 and ZmNCS2-23 localize in the plasma membrane, which confirmed their predicted membrane structures. These results provide a foundation for future studies regarding the functions of ZmNCS2 proteins, particularly those with potentially important roles in plant responses to abiotic stresses.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Weina Si
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, China
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14
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Abstract
L-ascorbic acid (vitamin C) is an essential metabolite in animals and plants due to its role as an enzyme co-factor and antioxidant activity. In most eukaryotic organisms, L-ascorbate is biosynthesized enzymatically, but in several major groups, including the primate suborder Haplorhini, this ability is lost due to gene truncations in the gene coding for L-gulonolactone oxidase. Specific ascorbate transporters (SVCTs) have been characterized only in mammals and shown to be essential for life. These belong to an extensively studied transporter family, called Nucleobase-Ascorbate Transporters (NAT). The prototypic member of this family, and one of the most extensively studied eukaryotic transporters, is UapA, a uric acid-xanthine/H+ symporter in the fungus Aspergillus nidulans. Here, we investigate molecular aspects of NAT substrate specificity and address the evolution of ascorbate transporters apparently from ancestral nucleobase transporters. We present a phylogenetic analysis, identifying a distinct NAT clade that includes all known L-ascorbate transporters. This clade includes homologues only from vertebrates, and has no members in non-vertebrate or microbial eukaryotes, plants or prokaryotes. Additionally, we identify within the substrate-binding site of NATs a differentially conserved motif, which we propose is critical for nucleobase versus ascorbate recognition. This conclusion is supported by the amino acid composition of this motif in distinct phylogenetic clades and mutational analysis in the UapA transporter. Together with evidence obtained herein that UapA can recognize with extremely low affinity L-ascorbate, our results support that ascorbate-specific NATs evolved by optimization of a sub-function of ancestral nucleobase transporters.
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Affiliation(s)
- Anezia Kourkoulou
- 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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15
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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de Vries RP, Riley R, Wiebenga A, Aguilar-Osorio G, Amillis S, Uchima CA, Anderluh G, Asadollahi M, Askin M, Barry K, Battaglia E, Bayram Ö, Benocci T, Braus-Stromeyer SA, Caldana C, Cánovas D, Cerqueira GC, Chen F, Chen W, Choi C, Clum A, dos Santos RAC, Damásio ARDL, Diallinas G, Emri T, Fekete E, Flipphi M, Freyberg S, Gallo A, Gournas C, Habgood R, Hainaut M, Harispe ML, Henrissat B, Hildén KS, Hope R, Hossain A, Karabika E, Karaffa L, Karányi Z, Kraševec N, Kuo A, Kusch H, LaButti K, Lagendijk EL, Lapidus A, Levasseur A, Lindquist E, Lipzen A, Logrieco AF, MacCabe A, Mäkelä MR, Malavazi I, Melin P, Meyer V, Mielnichuk N, Miskei M, Molnár ÁP, Mulé G, Ngan CY, Orejas M, Orosz E, Ouedraogo JP, Overkamp KM, Park HS, Perrone G, Piumi F, Punt PJ, Ram AFJ, Ramón A, Rauscher S, Record E, Riaño-Pachón DM, Robert V, Röhrig J, Ruller R, Salamov A, Salih NS, Samson RA, Sándor E, Sanguinetti M, Schütze T, Sepčić K, Shelest E, Sherlock G, Sophianopoulou V, Squina FM, Sun H, Susca A, Todd RB, Tsang A, Unkles SE, van de Wiele N, van Rossen-Uffink D, Oliveira JVDC, Vesth TC, Visser J, Yu JH, Zhou M, Andersen MR, Archer DB, Baker SE, Benoit I, Brakhage AA, Braus GH, Fischer R, Frisvad JC, Goldman GH, Houbraken J, Oakley B, Pócsi I, Scazzocchio C, Seiboth B, vanKuyk PA, Wortman J, Dyer PS, Grigoriev IV. Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus. Genome Biol 2017; 18:28. [PMID: 28196534 PMCID: PMC5307856 DOI: 10.1186/s13059-017-1151-0] [Citation(s) in RCA: 311] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/10/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. RESULTS We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. CONCLUSIONS Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.
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Affiliation(s)
- Ronald P. de Vries
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Robert Riley
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ad Wiebenga
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Guillermo Aguilar-Osorio
- Department of Food Science and Biotechnology, Faculty of Chemistry, National University of Mexico, Ciudad Universitaria, D.F. C.P. 04510 Mexico
| | - Sotiris Amillis
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Cristiane Akemi Uchima
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Present address: VTT Brasil, Alameda Inajá, 123, CEP 06460-055 Barueri, São Paulo Brazil
| | - Gregor Anderluh
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Mojtaba Asadollahi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Marion Askin
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: CSIRO Publishing, Unipark, Building 1 Level 1, 195 Wellington Road, Clayton, VIC 3168 Australia
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Evy Battaglia
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Özgür Bayram
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Biology, Maynooth University, Maynooth, Co. Kildare Ireland
| | - Tiziano Benocci
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Susanna A. Braus-Stromeyer
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Camila Caldana
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Max Planck Partner Group, Brazilian Bioethanol Science and Technology Laboratory, CEP 13083-100 Campinas, Sao Paulo Brazil
| | - David Cánovas
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Fungal Genetics and Genomics Unit, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences (BOKU) Vienna, Vienna, Austria
| | | | - Fusheng Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Wanping Chen
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Cindy Choi
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Alicia Clum
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Renato Augusto Corrêa dos Santos
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - André Ricardo de Lima Damásio
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
- Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, CEP 13083-862 Campinas, SP Brazil
| | - George Diallinas
- Department of Biology, National and Kapodistrian University of Athens, Panepistimioupolis, 15781 Athens, Greece
| | - Tamás Emri
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Erzsébet Fekete
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Michel Flipphi
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Susanne Freyberg
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Antonia Gallo
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), via Provinciale Lecce-Monteroni, 73100 Lecce, Italy
| | - Christos Gournas
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
- Present address: Université Libre de Bruxelles Institute of Molecular Biology and Medicine (IBMM), Brussels, Belgium
| | - Rob Habgood
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | | | - María Laura Harispe
- Institut Pasteur de Montevideo, Unidad Mixta INIA-IPMont, Mataojo 2020, CP11400 Montevideo, Uruguay
- Present address: Instituto de Profesores Artigas, Consejo de Formación en Educación, ANEP, CP 11800, Av. del Libertador 2025, Montevideo, Uruguay
| | - Bernard Henrissat
- CNRS, Aix-Marseille Université, Marseille, France
- INRA, USC 1408 AFMB, 13288 Marseille, France
- Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kristiina S. Hildén
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Ryan Hope
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Abeer Hossain
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Eugenia Karabika
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
- Present Address: Department of Chemistry, University of Ioannina, Ioannina, 45110 Greece
| | - Levente Karaffa
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsolt Karányi
- Department of Medicine, Faculty of Medicine, University of Debrecen, Nagyerdei krt. 98, 4032 Debrecen, Hungary
| | - Nada Kraševec
- Laboratory for Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia
| | - Alan Kuo
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Harald Kusch
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
- Department of Medical Informatics, University Medical Centre, Robert-Koch-Str.40, 37075 Göttingen, Germany
- Department of Molecular Biology, Universitätsmedizin Göttingen, Humboldtallee 23, Göttingen, 37073 Germany
| | - Kurt LaButti
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Ellen L. Lagendijk
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Alla Lapidus
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
- Present address: Center for Algorithmic Biotechnology, St.Petersburg State University, St. Petersburg, Russia
| | - Anthony Levasseur
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE), UM63, CNRS 7278, IRD 198, INSERM U1095, IHU Méditerranée Infection, Pôle des Maladies Infectieuses, Assistance Publique-Hôpitaux de Marseille, Faculté de Médecine, 27 Bd Jean Moulin, 13005 Marseille, France
| | - Erika Lindquist
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Anna Lipzen
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonio F. Logrieco
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Andrew MacCabe
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Miia R. Mäkelä
- Department of Food and Environmental Sciences, University of Helsinki, Viikinkaari 9, Helsinki, Finland
| | - Iran Malavazi
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, São Paulo Brazil
| | - Petter Melin
- Uppsala BioCenter, Department of Microbiology, Swedish University of Agricultural Sciences, P.O. Box 7025, 750 07 Uppsala, Sweden
- Present address: Swedish Chemicals Agency, Box 2, 172 13 Sundbyberg, Sweden
| | - Vera Meyer
- Institute of Biotechnology, Department Applied and Molecular Microbiology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Natalia Mielnichuk
- Department of Genetics, Faculty of Biology, University of Seville, Avda de Reina Mercedes 6, 41012 Sevilla, Spain
- Present address: Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, CONICET, Saladillo 2468 C1440FFX, Ciudad de Buenos Aires, Argentina
| | - Márton Miskei
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
- MTA-DE Momentum, Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Nagyerdei krt.98., 4032 Debrecen, Hungary
| | - Ákos P. Molnár
- Department of Biochemical Engineering, Faculty of Science and Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Giuseppina Mulé
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Chew Yee Ngan
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Margarita Orejas
- Departamento de Biotecnología, Instituto de Agroquímica y Tecnología de Alimentos, Consejo Superior de Investigaciones Científicas (CSIC), Paterna, Valencia, Spain
| | - Erzsébet Orosz
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Jean Paul Ouedraogo
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Karin M. Overkamp
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, 702-701 Republic of Korea
| | - Giancarlo Perrone
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Francois Piumi
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
- Present address: INRA UMR1198 Biologie du Développement et de la Reproduction - Domaine de Vilvert, Jouy en Josas, 78352 Cedex France
| | - Peter J. Punt
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Dutch DNA Biotech BV, Utrechtseweg 48, 3703AJ Zeist, The Netherlands
| | - Arthur F. J. Ram
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Ramón
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Stefan Rauscher
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Eric Record
- INRA, Aix-Marseille Univ, BBF, Biodiversité et Biotechnologie Fongiques, Marseille, France
| | - Diego Mauricio Riaño-Pachón
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Vincent Robert
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Julian Röhrig
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Roberto Ruller
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Asaf Salamov
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Nadhira S. Salih
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
- Department of Biology, School of Science, University of Sulaimani, Al Sulaymaneyah, Iraq
| | - Rob A. Samson
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Erzsébet Sándor
- Institute of Food Science, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary
| | - Manuel Sanguinetti
- Sección Bioquímica, Departamento de Biología Celular y Molecular, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Tabea Schütze
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: Department Applied and Molecular Microbiology, Institute of Biotechnology, Berlin University of Technology, Gustav-Meyer-Allee 25, 13355 Berlin, Germany
| | - Kristina Sepčić
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia
| | - Ekaterina Shelest
- Systems Biology/Bioinformatics group, Leibniz Institute for Natural Product Research and Infection Biology, Hans Knoell Institute, (HKI), Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gavin Sherlock
- Department of Genetics, Stanford University, Stanford, CA 94305-5120 USA
| | - Vicky Sophianopoulou
- Institute of Biosciences and Applications, Microbial Molecular Genetics Laboratory, National Center for Scientific Research, Demokritos (NCSRD), Athens, Greece
| | - Fabio M. Squina
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Hui Sun
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
| | - Antonia Susca
- Institute of Sciences of Food Production (ISPA), National Research Council (CNR), Via Amendola 122/O, 70126 Bari, Italy
| | - Richard B. Todd
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506 USA
| | - Adrian Tsang
- Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke Street West, Montreal, QC H4B 1R6 Canada
| | - Shiela E. Unkles
- School of Biology, University of St Andrews, St Andrews, Fife KY16 9TH UK
| | - Nathalie van de Wiele
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Diana van Rossen-Uffink
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
- Present address: BaseClear B.V., Einsteinweg 5, 2333 CC Leiden, The Netherlands
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Ciência e Tecnologia do Bioetanol (CTBE), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Caixa Postal 6192 CEP 13083-970, Campinas, São Paulo Brasil
| | - Tammi C. Vesth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Jaap Visser
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Jae-Hyuk Yu
- Departments of Bacteriology and Genetics, University of Wisconsin-Madison, 1550 Linden Drive, Madison, WI 53706 USA
| | - Miaomiao Zhou
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Mikael R. Andersen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - David B. Archer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Scott E. Baker
- Fungal Biotechnology Team, Pacific Northwest National Laboratory, Richland, Washington, 99352 USA
| | - Isabelle Benoit
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Fungal Molecular Physiology, Utrecht University, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Present address: Centre of Functional and Structure Genomics Biology Department Concordia University, 7141 Sherbrooke St. W., Montreal, QC H4B 1R6 Canada
| | - Axel A. Brakhage
- Department of Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology - Hans Knoell Institute (HKI) and Institute for Microbiology, Friedrich Schiller University Jena, Beutenbergstr. 11a, 07745 Jena, Germany
| | - Gerhard H. Braus
- Department of Molecular Microbiology and Genetics, Institute for Microbiology and Genetics, Georg August University Göttingen, Grisebachstr. 8, 37077 Göttingen, Germany
| | - Reinhard Fischer
- Department of Microbiology, Karlsruhe Institute of Technology, Institute for Applied Biosciences, Hertzstrasse 16,, 76187 Karlsruhe, Germany
| | - Jens C. Frisvad
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads 223, 2800 Kongens Lyngby, Denmark
| | - Gustavo H. Goldman
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Av. do Café S/N, CEP 14040-903 Ribeirão Preto, São Paulo Brazil
| | - Jos Houbraken
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
| | - Berl Oakley
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas 66045 USA
| | - István Pócsi
- Department of Biotechnology and Microbiology, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, 4032 Debrecen, Hungary
| | - Claudio Scazzocchio
- Department of Microbiology, Imperial College, London, SW7 2AZ UK
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, University Paris‐Sud, Université Paris‐Saclay, 91198 Gif‐sur‐Yvette cedex, France
| | - Bernhard Seiboth
- Research Division Biochemical Technology, Institute of Chemical Engineering, TU Wien, Gumpendorferstraße 1a, 1060 Vienna, Austria
| | - Patricia A. vanKuyk
- Westerdijk Fungal Biodiversity Institute, Uppsalalaan 8, 3584 CT Utrecht, The Netherlands
- Institute of Biology Leiden, Molecular Microbiology and Biotechnology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Jennifer Wortman
- Broad Institute, 415 Main St, Cambridge, MA 02142 USA
- Present address: Seres Therapeutics, 200 Sidney St, Cambridge, MA 02139 USA
| | - Paul S. Dyer
- School of Life Sciences, University of Nottingham, University Park, Nottingham, NG7 2RD UK
| | - Igor V. Grigoriev
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598 USA
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Diallinas G. Dissection of Transporter Function: From Genetics to Structure. Trends Genet 2016; 32:576-90. [DOI: 10.1016/j.tig.2016.06.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [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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18
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Daumann M, Golfier P, Knüppel N, Hahn M, Möhlmann T. Botrytis cinerea can import and utilize nucleosides in salvage and catabolism and BcENT functions as high affinity nucleoside transporter. Fungal Biol 2016; 120:904-916. [PMID: 27521624 DOI: 10.1016/j.funbio.2016.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 04/13/2016] [Accepted: 05/31/2016] [Indexed: 10/21/2022]
Abstract
Nucleotide de novo synthesis is an essential pathway in nearly all organisms. Transport processes as well as salvage and catabolism of nucleotides and pathway intermediates are required to balance nucleotide pools. We have analysed the genome of the fungal plant pathogen Botrytis cinerea for genes involved in nucleotide metabolism and found a complete set of genes necessary for purine and pyrimidine uptake and salvage based on homology of the gene products to corresponding proteins from Aspergillus nidulans. Candidate genes required for a complete purine catabolic sequence were identified in addition. These analyses were complemented by growth tests showing functional transport and salvage activity for pyrimidines. Growth of B. cinerea mycelium in nitrogen free medium could be restored by addition of purines, indicating the presence of a functional purine catabolism, whereas pyrimidines did not support growth. Bcin07g05490 (BcENT) was identified as sole member of the equilibrative nucleoside transporter (ENT) family. The protein synthesized in Saccharomyces cerevisiae revealed high affinity transport of adenosine (KM = 6.81 μM) and uridine (KM=9.04 μM). Furthermore, a BcENT knockout mutant was generated and tested in a range of growth and infection assays. These results provide detailed insight in the use of externally supplied nucleobases and nucleosides by B. cinerea.
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Affiliation(s)
- Manuel Daumann
- Pflanzenphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Philippe Golfier
- Pflanzenphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Nathalie Knüppel
- Phytopathologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Matthias Hahn
- Phytopathologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Torsten Möhlmann
- Pflanzenphysiologie, Fachbereich Biologie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany.
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Alguel Y, Amillis S, Leung J, Lambrinidis G, Capaldi S, Scull NJ, Craven G, Iwata S, Armstrong A, Mikros E, Diallinas G, Cameron AD, Byrne B. Structure of eukaryotic purine/H(+) symporter UapA suggests a role for homodimerization in transport activity. Nat Commun 2016; 7:11336. [PMID: 27088252 DOI: 10.1038/ncomms11336] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 03/16/2016] [Indexed: 02/03/2023] Open
Abstract
The uric acid/xanthine H+ symporter, UapA, is a high-affinity purine transporter from the filamentous fungus Aspergillus nidulans. Here we present the crystal structure of a genetically stabilized version of UapA (UapA-G411VΔ1–11) in complex with xanthine. UapA is formed from two domains, a core domain and a gate domain, similar to the previously solved uracil transporter UraA, which belongs to the same family. The structure shows UapA in an inward-facing conformation with xanthine bound to residues in the core domain. Unlike UraA, which was observed to be a monomer, UapA forms a dimer in the crystals with dimer interactions formed exclusively through the gate domain. Analysis of dominant negative mutants is consistent with dimerization playing a key role in transport. We postulate that UapA uses an elevator transport mechanism likely to be shared with other structurally homologous transporters including anion exchangers and prestin. UapA is a uric acid/xanthine H+ symporter from a filamentous fungus. Here, the authors solve the crystal structure of the transporter in complex with xanthine revealing it to be a dimer, and this homodimerisation is proposed to be important for function.
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20
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Evangelinos M, Martzoukou O, Chorozian K, Amillis S, Diallinas G. BsdA(Bsd2) -dependent vacuolar turnover of a misfolded version of the UapA transporter along the secretory pathway: prominent role of selective autophagy. Mol Microbiol 2016; 100:893-911. [PMID: 26917498 DOI: 10.1111/mmi.13358] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2016] [Indexed: 12/13/2022]
Abstract
Transmembrane proteins translocate cotranslationally in the endoplasmic reticulum (ER) membrane and traffic as vesicular cargoes, via the Golgi, in their final membrane destination. Misfolding in the ER leads to protein degradation basically through the ERAD/proteasome system. Here, we use a mutant version of the purine transporter UapA (ΔR481) to show that specific misfolded versions of plasma membrane cargoes undergo vacuolar turnover prior to localization in the plasma membrane. We show that non-endocytic vacuolar turnover of ΔR481 is dependent on BsdA(Bsd2) , an ER transmembrane adaptor of HulA(Rsp5) ubiquitin ligase. We obtain in vivo evidence that BsdA(Bsd2) interacts with HulA(Rsp5) and ΔR481, primarily in the ER. Importantly, accumulation of ΔR481 in the ER triggers delivery of the selective autophagy marker Atg8 in vacuoles along with ΔR481. Genetic block of autophagy (atg9Δ, rabO(ts) ) reduces, but does not abolish, sorting of ΔR481 in the vacuoles, suggesting that a fraction of the misfolded transporter might be redirected for vacuolar degradation via the Golgi. Our results support that multiple routes along the secretory pathway operate for the detoxification of Aspergillus nidulans cells from misfolded membrane proteins and that BsdA is a key factor for marking specific misfolded cargoes.
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Affiliation(s)
- Minoas Evangelinos
- Faculty of Biology, University of Athens, Panepistimioupolis, 15784, Athens, Greece
| | - Olga Martzoukou
- Faculty of Biology, University of Athens, Panepistimioupolis, 15784, Athens, Greece
| | - Koar Chorozian
- Faculty of Biology, University of Athens, Panepistimioupolis, 15784, Athens, Greece
| | - Sotiris Amillis
- Faculty of Biology, University of Athens, Panepistimioupolis, 15784, Athens, Greece
| | - George Diallinas
- Faculty of Biology, University of Athens, Panepistimioupolis, 15784, Athens, Greece
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21
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Martzoukou O, Karachaliou M, Yalelis V, Leung J, Byrne B, Amillis S, Diallinas G. Oligomerization of the UapA Purine Transporter Is Critical for ER-Exit, Plasma Membrane Localization and Turnover. J Mol Biol 2015; 427:2679-96. [DOI: 10.1016/j.jmb.2015.05.021] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 11/29/2022]
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22
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Kalli AC, Sansom MSP, Reithmeier RAF. Molecular dynamics simulations of the bacterial UraA H+-uracil symporter in lipid bilayers reveal a closed state and a selective interaction with cardiolipin. PLoS Comput Biol 2015; 11:e1004123. [PMID: 25729859 PMCID: PMC4346270 DOI: 10.1371/journal.pcbi.1004123] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 01/09/2015] [Indexed: 11/25/2022] Open
Abstract
The Escherichia coli UraA H+-uracil symporter is a member of the nucleobase/ascorbate transporter (NAT) family of proteins, and is responsible for the proton-driven uptake of uracil. Multiscale molecular dynamics simulations of the UraA symporter in phospholipid bilayers consisting of: 1) 1-palmitoyl 2-oleoyl-phosphatidylcholine (POPC); 2) 1-palmitoyl 2-oleoyl-phosphatidylethanolamine (POPE); and 3) a mixture of 75% POPE, 20% 1-palmitoyl 2-oleoyl-phosphatidylglycerol (POPG); and 5% 1-palmitoyl 2-oleoyl-diphosphatidylglycerol/cardiolipin (CL) to mimic the lipid composition of the bacterial inner membrane, were performed using the MARTINI coarse-grained force field to self-assemble lipids around the crystal structure of this membrane transport protein, followed by atomistic simulations. The overall fold of the protein in lipid bilayers remained similar to the crystal structure in detergent on the timescale of our simulations. Simulations were performed in the absence of uracil, and resulted in a closed state of the transporter, due to relative movement of the gate and core domains. Anionic lipids, including POPG and especially CL, were found to associate with UraA, involving interactions between specific basic residues in loop regions and phosphate oxygens of the CL head group. In particular, three CL binding sites were identified on UraA: two in the inner leaflet and a single site in the outer leaflet. Mutation of basic residues in the binding sites resulted in the loss of CL binding in the simulations. CL may play a role as a “proton trap” that channels protons to and from this transporter within CL-enriched areas of the inner bacterial membrane. Symporters are proteins that are responsible for the co-transport of ions and small molecule solutes across cell membranes. UraA is an example of a symporter, and is responsible for the proton-driven uptake of uracil in bacteria like E. coli. Despite its importance as a member of a large family of nucleobase/ascorbate transporters (NAT) and the existence of structural and functional data, the mechanism by which UraA transports uracil across the bacterial membrane, and in particular the role of its diverse and complex lipid environment in the transport mechanism, remains elusive. In this study, we have used a multiscale computational methodology to examine the dynamics of UraA and to elucidate its interactions with lipids that resemble its native environment in the bacterial inner membrane. Our results demonstrate that negatively-charged lipids in the membrane (phosphatidylglycerol and cardiolipin) associate preferentially with UraA and may play a role in its function. Additionally, our simulations resulted in a closed state of UraA, a likely intermediate in the transport mechanism that may not be readily accessible by experimental methods.
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Affiliation(s)
- Antreas C. Kalli
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Krypotou E, Scazzocchio C, Diallinas G. 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] [What about the content of this article? (0)] [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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24
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Niopek-Witz S, Deppe J, Lemieux MJ, Möhlmann T. Biochemical characterization and structure–function relationship of two plant NCS2 proteins, the nucleobase transporters NAT3 and NAT12 from Arabidopsis thaliana. Biochimica et Biophysica Acta (BBA) - Biomembranes 2014; 1838:3025-35. [DOI: 10.1016/j.bbamem.2014.08.013] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 07/30/2014] [Accepted: 08/09/2014] [Indexed: 11/28/2022]
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25
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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26
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Girke C, Daumann M, Niopek-Witz S, Möhlmann T. Nucleobase and nucleoside transport and integration into plant metabolism. Front Plant Sci 2014; 5:443. [PMID: 25250038 PMCID: PMC4158802 DOI: 10.3389/fpls.2014.00443] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Diallinas G. Allopurinol and xanthine use different translocation mechanisms and trajectories in the fungal UapA transporter. Biochimie 2013; 95:1755-64. [PMID: 23791789 DOI: 10.1016/j.biochi.2013.05.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 05/31/2013] [Indexed: 01/14/2023]
Abstract
In Aspergillus nidulans UapA is a H(+)-driven transporter specific for xanthine, uric acid and several analogues. Here, genetic and physiological evidence is provided showing that allopurinol is a high-affinity, low-capacity, substrate for UapA. Surprisingly however, transport kinetic measurements showed that, uniquely among all recognized UapA substrates, allopurinol is transported by apparent facilitated diffusion and exhibits a paradoxical effect on the transport of physiological substrates. Specifically, excess xanthine or other UapA substrates inhibit allopurinol uptake, as expected, but the presence of excess allopurinol results in a concentration-dependent enhancement of xanthine binding and transport. Flexible docking approaches failed to detect allopurinol binding in the major UapA substrate binding site, which was recently identified by mutational analysis and substrate docking using all other UapA substrates. These results and genetic evidence suggest that the allopurinol translocation pathway is distinct from, but probably overlapping with, that of physiological UapA substrates. Furthermore, although the stimulating effect of allopurinol on xanthine transport could, in principle, be rationalized by a cryptic allopurinol-specific allosteric site, evidence was obtained supporting that accelerated influx of xanthine is triggered through exchange with cytoplasmically accumulated allopurinol. Our results are in line with recently accumulating evidence revealing atypical and complex mechanisms underlying transport systems.
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29
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Bürzle M, Suzuki Y, Ackermann D, Miyazaki H, Maeda N, Clémençon B, Burrier R, Hediger MA. The sodium-dependent ascorbic acid transporter family SLC23. Mol Aspects Med 2013; 34:436-54. [PMID: 23506882 DOI: 10.1016/j.mam.2012.12.002] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/16/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Marc Bürzle
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
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30
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Karachaliou M, Amillis S, Evangelinos M, Kokotos AC, Yalelis V, Diallinas G. The arrestin-like protein ArtA is essential for ubiquitination and endocytosis of the UapA transporter in response to both broad-range and specific signals. Mol Microbiol 2013; 88:301-17. [DOI: 10.1111/mmi.12184] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/12/2013] [Indexed: 12/16/2022]
Affiliation(s)
- Mayia Karachaliou
- Faculty of Biology; University of Athens; Panepistimiopolis 15784; Athens; Greece
| | - Sotiris Amillis
- Faculty of Biology; University of Athens; Panepistimiopolis 15784; Athens; Greece
| | - Minoas Evangelinos
- Faculty of Biology; University of Athens; Panepistimiopolis 15784; Athens; Greece
| | | | - Vassilis Yalelis
- Faculty of Biology; University of Athens; Panepistimiopolis 15784; Athens; Greece
| | - George Diallinas
- Faculty of Biology; University of Athens; Panepistimiopolis 15784; Athens; Greece
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Krypotou E, Diallinas G. Transport Assays in Aspergillus nidulans. Bio Protoc 2013. [DOI: 10.21769/bioprotoc.971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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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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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36
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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] [What about the content of this article? (0)] [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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bitsikas V, Karachaliou M, Gournas C, Diallinas G. Hypertonic conditions trigger transient plasmolysis, growth arrest and blockage of transporter endocytosis in Aspergillus nidulans and Saccharomyces cerevisiae. Mol Membr Biol 2010; 28:54-68. [PMID: 20919858 DOI: 10.3109/09687688.2010.510484] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
By using Aspergillus nidulans strains expressing functional GFP-tagged transporters under hypertonic conditions, we noticed the rapid appearance of cortical, relatively static, fluorescent patches (0.5-2.3 μm). These patches do not correspond to transporter microdomains as they co-localize with other plasma membrane-associated molecules, such as the pleckstrin homology (PH) domain and the SsoA t-Snare, or the lipophilic markers FM4-64 and filipin. In addition, they do not show characteristics of lipid rafts, MCCs or other membrane microdomains. Deconvoluted microscopic images showed that fluorescent patches correspond to plasma membrane invaginations. Transporters remain fully active during this phenomenon of localized plasmolysis. Plasmolysis was however associated with reduced growth rate and a dramatic blockage in transporter and FM4-64 endocytosis. These phenomena are transient and rapidly reversible upon wash-out of hypertonic media. Based on the observation that block in endocytosis by hypertonic treatment altered dramatically the cellular localization of tropomyosin (GFP-TpmA), although it did not affect the cortical appearance of upstream (SlaB-GFP) or downstream (AbpA-mRFP) endocytic components, we conclude that hypertonicity modifies actin dynamics and thus acts indirectly on endocytosis. This was further supported by the effect of latrunculin B, an actin depolymerization agent, on endocytosis. We show that the phenomena observed in A. nidulans also occur in Saccharomyces cerevisiae, suggesting that they constitute basic homeostatic responses of ascomycetes to hypertonic shock. Finally, our work shows that hypertonic treatments can be used as physiological tools to study the endocytic down-regulation of transporters in A. nidulans, as non-conditional genetic blocks affecting endocytic internalization are lethal or severely debilitating.
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Affiliation(s)
- Vassilis Bitsikas
- Faculty of Biology, Department of Botany, University of Athens, Panepistimioupolis, Athens, Greece
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Georgopoulou E, Mermelekas G, Karena E, Frillingos S. Purine substrate recognition by the nucleobase-ascorbate transporter signature motif in the YgfO xanthine permease: ASN-325 binds and ALA-323 senses substrate. J Biol Chem 2010; 285:19422-33. [PMID: 20406814 DOI: 10.1074/jbc.m110.120543] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The nucleobase-ascorbate transporter (NAT) signature motif is a conserved 11-amino acid sequence of the ubiquitous NAT/NCS2 family, essential for function and selectivity of both a bacterial (YgfO) and a fungal (UapA) purine-transporting homolog. We examined the role of NAT motif in more detail, using Cys-scanning and site-directed alkylation analysis of the YgfO xanthine permease of Escherichia coli. Analysis of single-Cys mutants in the sequence 315-339 for sensitivity to inactivation by 2-sulfonatoethyl methanethiosulfonate (MTSES(-)) and N-ethylmaleimide (NEM) showed a similar pattern: highly sensitive mutants clustering at the motif sequence (323-329) and a short alpha-helical face downstream (332, 333, 336). In the presence of substrate, N325C is protected from alkylation with either MTSES(-) or NEM, whereas sensitivity of A323C to inactivation by NEM is enhanced, shifting IC(50) from 34 to 14 microM. Alkylation or sensitivity of the other mutants is unaffected by substrate; the lack of an effect on Q324C is attributed to gross inability of this mutant for high affinity binding. Site-directed mutants G333R and S336N at the alpha-helical face downstream the motif display specific changes in ligand recognition relative to wild type; G333R allows binding of 7-methyl and 8-methylxanthine, whereas S336N disrupts affinity for 6-thioxanthine. Finally, all assayable motif-mutants are highly accessible to MTSES(-) from the periplasmic side. The data suggest that the NAT motif region lines the solvent- and substrate-accessible inner cavity, Asn-325 is at the binding site, Ala-323 responds to binding with a specific conformational shift, and Gly-333 and Ser-336 form part of the purine permeation pathway.
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Affiliation(s)
- Ekaterini Georgopoulou
- Laboratory of Biological Chemistry, University of Ioannina Medical School, 45110 Ioannina, Greece
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41
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Kosti V, Papageorgiou I, Diallinas G. Dynamic Elements at Both Cytoplasmically and Extracellularly Facing Sides of the UapA Transporter Selectively Control the Accessibility of Substrates to Their Translocation Pathway. J Mol Biol 2010; 397:1132-43. [DOI: 10.1016/j.jmb.2010.02.037] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Revised: 02/17/2010] [Accepted: 02/19/2010] [Indexed: 02/06/2023]
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Leung J, Karachaliou M, Alves C, Diallinas G, Byrne B. Expression and purification of a functional uric acid-xanthine transporter (UapA). Protein Expr Purif 2010; 72:139-46. [PMID: 20153431 DOI: 10.1016/j.pep.2010.02.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/03/2010] [Indexed: 11/19/2022]
Abstract
The Nucleobase-Ascorbate Transporters (NATs) family includes carriers with fundamental functions in uptake of key cellular metabolites, such as uric acid or vitamin C. The best studied example of a NAT transporter is the uric acid-xanthine permease (UapA) from the model ascomycete Aspergillus nidulans. Detailed genetic and biochemical analyses have revealed much about the mechanism of action of this protein; however, the difficulties associated with handling eukaryotic membrane proteins have limited efforts to elucidate the precise structure-function relationships of UapA by structural analysis. In this manuscript, we describe the heterologous overexpression of functional UapA as a fusion with GFP in different strains of Saccharomyces cerevisiae. The UapA-GFP construct expressed to 2.3 mg/L in a pep4Delta deletion strain lacking a key vacuolar endopeptidase and 3.8 mg/L in an npi1-1 mutant strain with defective Rsp5 ubiquitin ligase activity. Epifluorescence microscopy revealed that the UapA-GFP was predominately localized to the plasma membrane in both strains, although a higher intensity of fluorescence was observed for the npi1-1 mutant strain plasma membrane. In agreement with these observations, the npi1-1 mutant strain demonstrated a approximately 5-fold increase in uptake of [(3)H]-xanthine compared to the pep4Delta deletion strain. Despite yielding the best results for functional expression, in-gel fluorescence of the UapA-GFP expressed in the npi1-1 mutant strain revealed that the protein was subject to significant proteolytic degradation. Large scale expression of the protein using the pep4Delta deletion strain followed by purification produced mg quantities of pure, monodispersed protein suitable for further structural and functional studies. In addition, this work has generated a yeast cell based system for performing reverse genetics and other targeted approaches, in order to further understand the mechanism of action of this important model protein.
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Affiliation(s)
- James Leung
- Division of Molecular Biology, Imperial College London, South Kensington, London SW7 2AZ, UK
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43
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Karena E, Frillingos S. Role of intramembrane polar residues in the YgfO xanthine permease: HIS-31 and ASN-93 are crucial for affinity and specificity, and ASP-304 and GLU-272 are irreplaceable. J Biol Chem 2009; 284:24257-68. [PMID: 19581302 DOI: 10.1074/jbc.m109.030734] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Using the YgfO xanthine permease of Escherichia coli as a bacterial model for the study of the evolutionarily ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family, we performed a systematic Cys-scanning and site-directed mutagenesis of 14 putatively charged (Asp, Glu, His, Lys, or Arg) and 7 highly polar (Gln or Asn) residues that are predicted to lie in transmembrane helices (TMs). Of 21 single-Cys mutants engineered in the background of a functional YgfO devoid of Cys residues (C-less), only four are inactive or have marginal activity (H31C, N93C, E272C, D304C). The 4 residues are conserved throughout the family in TM1 (His-31), TM3 (Asn-93/Ser/Thr), TM8 (Glu-272), and putative TM9a (Asp-304/Asn/Glu). Extensive site-directed mutagenesis in wild-type background showed that H31N and H31Q have high activity and affinity for xanthine but H31Q recognizes novel purine bases and analogues, whereas H31C and H31L have impaired affinity for xanthine and analogues, and H31K or H31R impairs expression in the membrane. N93S and N93A are highly active but more promiscuous for recognition of analogues at the imidazole moiety of substrate, N93D has low activity, N93T has low affinity for xanthine or analogues, and N93Q or N93C is inactive. All mutants replacing Glu-272 or Asp-304, including E272D, E272Q, D304E, and D304N, are inactive, although expressed to high levels in the membrane. Finally, one of the 17 assayable single-Cys mutants, Q258C, was sensitive to inactivation by N-ethylmaleimide. The findings suggest that polar residues important for the function of YgfO cluster in TMs 1, 3, 8 and 9a.
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Affiliation(s)
- Ekaterini Karena
- Laboratory of Biological Chemistry, University of Ioannina Medical School, 45110 Ioannina, Greece
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Hamari Z, Amillis S, Drevet C, Apostolaki A, Vágvölgyi C, Diallinas G, Scazzocchio C. Convergent evolution and orphan genes in the Fur4p-like family and characterization of a general nucleoside transporter inAspergillus nidulans. Mol Microbiol 2009; 73:43-57. [DOI: 10.1111/j.1365-2958.2009.06738.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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46
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Lemuh ND, Diallinas G, Frillingos S, Mermelekas G, Karagouni AD, Hatzinikolaou DG. Purification and partial characterization of the xanthine-uric acid transporter (UapA) of Aspergillus nidulans. Protein Expr Purif 2009; 63:33-9. [DOI: 10.1016/j.pep.2008.08.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 08/19/2008] [Accepted: 08/19/2008] [Indexed: 11/26/2022]
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47
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Papageorgiou I, Gournas C, Vlanti A, Amillis S, Pantazopoulou A, Diallinas G. Specific Interdomain Synergy in the UapA Transporter Determines Its Unique Specificity for Uric Acid among NAT Carriers. J Mol Biol 2008; 382:1121-35. [DOI: 10.1016/j.jmb.2008.08.005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2008] [Revised: 08/04/2008] [Accepted: 08/04/2008] [Indexed: 10/21/2022]
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Vlanti A, Diallinas G. The Aspergillus nidulans FcyB cytosine-purine scavenger is highly expressed during germination and in reproductive compartments and is downregulated by endocytosis. Mol Microbiol 2008; 68:959-77. [DOI: 10.1111/j.1365-2958.2008.06198.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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49
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Papakostas K, Georgopoulou E, Frillingos S. Cysteine-scanning Analysis of Putative Helix XII in the YgfO Xanthine Permease. J Biol Chem 2008; 283:13666-78. [DOI: 10.1074/jbc.m800261200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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50
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Goudela S, Reichard U, Amillis S, Diallinas G. Characterization and kinetics of the major purine transporters in Aspergillus fumigatus. Fungal Genet Biol 2008; 45:459-72. [PMID: 17881254 DOI: 10.1016/j.fgb.2007.08.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2007] [Revised: 07/30/2007] [Accepted: 08/01/2007] [Indexed: 11/30/2022]
Abstract
Three genes encoding putative purine transporters have been identified in silico in the genome of Aspergillus fumigatus by their very close similarity of their translation products to well-studied homologues in A. nidulans. Two of these transporters, called AfUapC and AfAzgA, were found responsible for bulk uptake of purines and studied in detail herein. Genetic knock-out analysis, regulation of transcription, direct purine uptake assays and heterologous expression in A. nidulans have unequivocally shown that AfUapC and AfAzgA are high-affinity, high-capacity, purine/H(+) symporters, the first being specific for xanthine, uric acid and oxypurinol, whereas the second for adenine, hypoxanthine, guanine and purine. The expression of these transporters is primarily controlled at the level of transcription. Transcription of both genes is purine-inducible, albeit with different efficiencies, whereas AfuapC is also ammonium-repressible. We characterised in detail the kinetics of the AfUapC and AfAzgA transporters, both in A. fumigatus and in A. nidulans, using a plethora of possible purine substrates. This analysis led us to propose kinetic models describing the molecular interactions of AfUapC and AfAzgA with purines. These models are discussed comparatively with analogous models from other purine transporters from fungi, bacteria and humans, and within the frame of a systematic development of novel purine-related antifungals.
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Affiliation(s)
- Sophia Goudela
- Faculty of Biology, Department of Botany, University of Athens, Panepistimioupolis, Athens 15781, Greece
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