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Ohnuki J, Okazaki KI. Integration of AlphaFold with Molecular Dynamics for Efficient Conformational Sampling of Transporter Protein NarK. J Phys Chem B 2024. [PMID: 39066727 DOI: 10.1021/acs.jpcb.4c02726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Transporter proteins carry their substrate across the cell membrane by changing their conformation. Thus, conformational dynamics are crucial for transport function. However, clarifying the complete transport cycle is challenging even with the current structural biology approach. Molecular dynamics (MD) simulation is a computational approach that can provide the time-resolved conformational dynamics of transporter proteins in atomic details but suffers from a high computational cost. Here, we integrate state-of-the-art protein structure prediction AI, AlphaFold2 (AF2), with MD simulation to reduce the computational cost. Focusing on the transporter protein NarK, we first show that AF2 sampled broad conformations of NarK, including the inward-open, occluded, and outward-open states. We also applied the coevolution-informed mutation in AF2, identifying state-shifting mutations. Then, we show that MD simulations from AF2-generated outward-open conformation, which is experimentally unresolved, captured the essence of the conformational state. We also found that MD simulations from AF2-generated intermediates showed transient dynamics like a transition state connecting two conformational states. This study paves the way for efficient conformational sampling of transporter proteins.
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Affiliation(s)
- Jun Ohnuki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Kei-Ichi Okazaki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, Aichi 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
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2
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Schmiege P, Donnelly L, Elghobashi-Meinhardt N, Lee CH, Li X. Structure and inhibition of the human lysosomal transporter Sialin. Nat Commun 2024; 15:4386. [PMID: 38782953 PMCID: PMC11116495 DOI: 10.1038/s41467-024-48535-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Sialin, a member of the solute carrier 17 (SLC17) transporter family, is unique in its ability to transport not only sialic acid using a pH-driven mechanism, but also transport mono and diacidic neurotransmitters, such as glutamate and N-acetylaspartylglutamate (NAAG), into synaptic vesicles via a membrane potential-driven mechanism. While most transporters utilize one of these mechanisms, the structural basis of how Sialin transports substrates using both remains unclear. Here, we present the cryogenic electron-microscopy structures of human Sialin: apo cytosol-open, apo lumen-open, NAAG-bound, and inhibitor-bound. Our structures show that a positively charged cytosol-open vestibule accommodates either NAAG or the Sialin inhibitor Fmoc-Leu-OH, while its luminal cavity potentially binds sialic acid. Moreover, functional analyses along with molecular dynamics simulations identify key residues in binding sialic acid and NAAG. Thus, our findings uncover the essential conformational states in NAAG and sialic acid transport, demonstrating a working model of SLC17 transporters.
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Affiliation(s)
- Philip Schmiege
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Linda Donnelly
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | | | - Chia-Hsueh Lee
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Xiaochun Li
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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3
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Wang S, Lan B, Yu L, Xiao M, Jiang L, Qin Y, Jin Y, Zhou Y, Armanbek G, Ma J, Wang M, Jetten MSM, Tian H, Zhu G, Zhu YG. Ammonium-derived nitrous oxide is a global source in streams. Nat Commun 2024; 15:4085. [PMID: 38744837 PMCID: PMC11094135 DOI: 10.1038/s41467-024-48343-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Global riverine nitrous oxide (N2O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N2O emissions. However, the mechanisms and pathways controlling hyporheic N2O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N2O sources (69.6 ± 2.1%) in agricultural streams around the world. The N2O fluxes are mainly in positive correlation with ammonia. The potential N2O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N2O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N2O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N2O emissions.
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Affiliation(s)
- Shanyun Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bangrui Lan
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Longbin Yu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Manyi Xiao
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Liping Jiang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Qin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yucheng Jin
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Yuting Zhou
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Gawhar Armanbek
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jingchen Ma
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Manting Wang
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Mike S M Jetten
- Department of Microbiology, Radboud University Nijmegen, Nijmegen, AJ, 6525, the Netherlands
| | - Hanqin Tian
- Center for Earth System Science and Global Sustainability, Schiller Institute for Integrated Science and Society, Boston College, Chestnut Hill, MA, 02467, USA
- Department of Earth and Environmental Sciences, Boston College, Chestnut Hill, MA, 02467, USA
| | - Guibing Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yong-Guan Zhu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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4
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Dong X, Yu J, Ye C, Liu D, Zou D, Han Z, Yu Q, Huang K, Li H, Wei X. Control of tobacco-specific nitrosamines by the Bacillus siamensis: Strain isolation, genome sequencing, mechanism analysis and genetic engineering. JOURNAL OF HAZARDOUS MATERIALS 2024; 469:133877. [PMID: 38452666 DOI: 10.1016/j.jhazmat.2024.133877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/03/2024] [Accepted: 02/22/2024] [Indexed: 03/09/2024]
Abstract
Nitrosamines are considered carcinogens that threaten human health and environment. Especially, high contents of Tobacco-specific nitrosamines (TSNAs) are generated during the fermentation process of cigar tobacco. To control the accumulation of TSNAs, one novel strain WD-32 was isolated by comprehensively evaluating the reduction characteristics of nitrate, nitrite, and TSNAs, and this strain was identified as Bacillus siamensis by 16 S rRNA gene analysis and MALDI-TOF MS evaluation. Subsequently, whole genome sequencing of B. siamensis WD-32 was carried out to excavate important genes and enzymes involved, and the possible reduction mechanism of TSNAs was explored. More importantly, the reduction of TSNAs by B. siamensis was significantly promoted by knockout of narG gene. During the practical agricultural fermentation process of the cigar tobacco leaves, the treatment by the WD-32∆narG cells resulted in a 60% reduction of the total TSNAs content compared with the control, and the concentrations of the NNN and NNK were decreased by 69% and 59%, respectively. In summary, this study offers efficient strains for reduction of the TSNAs in cigar tobacco, and provides new insights into the reduction mechanism of TSNAs, which will promote the application of microbial methods in control of TSNAs and nitrite.
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Affiliation(s)
- Xinyu Dong
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou 450001, China; State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jun Yu
- Tobacco Research Institute of Hubei Province, Wuhan 430062, China
| | - Changwen Ye
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou 450001, China.
| | - Dandan Liu
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou 450001, China
| | - Dian Zou
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhenying Han
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingru Yu
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kuo Huang
- Zhengzhou Tobacco Research Institute of China National Tobacco Corporation, Zhengzhou 450001, China
| | - Hao Li
- Tobacco Research Institute of Hubei Province, Wuhan 430062, China
| | - Xuetuan Wei
- State Key Laboratory of Agricultural Microbiology, College of Food Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
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5
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Ohnuki J, Jaunet-Lahary T, Yamashita A, Okazaki KI. Accelerated Molecular Dynamics and AlphaFold Uncover a Missing Conformational State of Transporter Protein OxlT. J Phys Chem Lett 2024; 15:725-732. [PMID: 38215403 DOI: 10.1021/acs.jpclett.3c03052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2024]
Abstract
Transporter proteins change their conformations to carry their substrate across the cell membrane. The conformational dynamics is vital to understanding the transport function. We have studied the oxalate transporter (OxlT), an oxalate:formate antiporter from Oxalobacter formigenes, significant in avoiding kidney stone formation. The atomic structure of OxlT has been recently solved in the outward-open and occluded states. However, the inward-open conformation is still missing, hindering a complete understanding of the transporter. Here, we performed a Gaussian accelerated molecular dynamics simulation to sample the extensive conformational space of OxlT and successfully predicted the inward-open conformation where cytoplasmic substrate formate binding was preferred over oxalate binding. We also identified critical interactions for the inward-open conformation. The results were complemented by an AlphaFold2 structure prediction. Although AlphaFold2 solely predicted OxlT in the outward-open conformation, mutation of the identified critical residues made it partly predict the inward-open conformation, identifying possible state-shifting mutations.
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Affiliation(s)
- Jun Ohnuki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
| | - Titouan Jaunet-Lahary
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
| | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| | - Kei-Ichi Okazaki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki 444-8585, Japan
- Graduate Institute for Advanced Studies, SOKENDAI, Okazaki, Aichi 444-8585, Japan
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6
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Mosley OE, Gios E, Handley KM. Implications for nitrogen and sulphur cycles: phylogeny and niche-range of Nitrospirota in terrestrial aquifers. ISME COMMUNICATIONS 2024; 4:ycae047. [PMID: 38650708 PMCID: PMC11033732 DOI: 10.1093/ismeco/ycae047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/20/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Increasing evidence suggests Nitrospirota are important contributors to aquatic and subsurface nitrogen and sulphur cycles. We determined the phylogenetic and ecological niche associations of Nitrospirota colonizing terrestrial aquifers. Nitrospirota compositions were determined across 59 groundwater wells. Distributions were strongly influenced by oxygen availability in groundwater, marked by a trade-off between aerobic (Nitrospira, Leptospirillum) and anaerobic (Thermodesulfovibrionia, unclassified) lineages. Seven Nitrospirota metagenome-assembled genomes (MAGs), or populations, were recovered from a subset of wells, including three from the recently designated class 9FT-COMBO-42-15. Most were relatively more abundant and transcriptionally active in dysoxic groundwater. These MAGs were analysed with 743 other Nitrospirota genomes. Results illustrate the predominance of certain lineages in aquifers (e.g. non-nitrifying Nitrospiria, classes 9FT-COMBO-42-15 and UBA9217, and Thermodesulfovibrionales family UBA1546). These lineages are characterized by mechanisms for nitrate reduction and sulphur cycling, and, excluding Nitrospiria, the Wood-Ljungdahl pathway, consistent with carbon-limited, low-oxygen, and sulphur-rich aquifer conditions. Class 9FT-COMBO-42-15 is a sister clade of Nitrospiria and comprises two families spanning a transition in carbon fixation approaches: f_HDB-SIOIB13 encodes rTCA (like Nitrospiria) and f_9FT-COMBO-42-15 encodes Wood-Ljungdahl CO dehydrogenase (like Thermodesulfovibrionia and UBA9217). The 9FT-COMBO-42-15 family is further differentiated by its capacity for sulphur oxidation (via DsrABEFH and SoxXAYZB) and dissimilatory nitrate reduction to ammonium, and gene transcription indicated active coupling of nitrogen and sulphur cycles by f_9FT-COMBO-42-15 in dysoxic groundwater. Overall, results indicate that Nitrospirota are widely distributed in groundwater and that oxygen availability drives the spatial differentiation of lineages with ecologically distinct roles related to nitrogen and sulphur metabolism.
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Affiliation(s)
- Olivia E Mosley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Present address: NatureMetrics Ltd, Surrey Research Park, Guildford GU2 7HJ, United Kingdom
| | - Emilie Gios
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
- Present address: NINA, Norwegian Institute for Nature Research, Trondheim 7034, Norway
| | - Kim M Handley
- School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand
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Luo Z, Li Y, Chen B, Lei M, Zhang N, Zhang X, Li J. Effect of free ammonia on partial denitrification: Long-term performance, mechanism, and feasibility of PD/Anammox-FBBR for mature landfill leachate treatment. WATER RESEARCH 2023; 243:120238. [PMID: 37506632 DOI: 10.1016/j.watres.2023.120238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 05/25/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023]
Abstract
As a stable and effective approach for NO2--N accumulation, partial denitrification (PD) could significantly cut down operation cost, and PD/Anammox (PD/A) is a promising nitrogen removal process in wastewater treatment. The biotoxicity of free ammonia (FA) to nitrifying bacteria and anammox bacteria has been demonstrated, while whether FA affects PD bacteria is an open question. Here, long-term operation of PD-fixed bed biofilm reactor (PD-FBBR) treating synthetic wastewater and mature landfill leachate was conducted to reveal the mechanism concerning the effect of FA on PD bacteria. Stable NO2--N accumulation was achieved with NO3--N to NO2--N transformation ratio (NTR) of 60-70% during 280-day operation with FA ranged from 0 to 20.71 ± 0.23 mg/L, while NTR decreased and maintained at ∼30% when FA reached 40.59 ± 0.19 mg/L. Specific NOx--N reduction rate improved at low FA concentration (< 12 mg/L), while high FA level (> 25 mg/L) had inhibitory effect on PD bacteria. Under FA stress, more extracellular polymeric substances (EPS) were secreted, and the glnA gene abundance, glutamine synthase concentration, and glutamine concentration in cell and EPS significantly increased, indicating the enhancement of glutamine biosynthesis in PD bacteria for ammonia assimilation played an important role in response to FA stress. Metagenomic sequencing showed that FA stimulated the upregulation of narK (NO3--N/NO2--N antiporter) gene abundance and enhanced uptake of NO3--N and extrusion of NO2--N. Comamonas, unclassified_f__Comamonadaceae and Thauera were highly enriched in biofilm, which played a key role in the stable NO2--N accumulation. Furthermore, a novel two stage PD/A-FBBR was applied to mature landfill leachate treatment, and satisfactory total inorganic nitrogen removal efficiency ranged from 81.38 ± 3.56% to 89.16 ± 1.57% was obtained at relatively low COD/NO3--N of 2.57-2.84. Overall, these findings demonstrated how PD bacteria respond to FA stress and confirmed the feasibility of PD/A process in high FA wastewater treatment.
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Affiliation(s)
- Zhizhan Luo
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Yong Li
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Bohan Chen
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Mengen Lei
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Naixin Zhang
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Xiaolei Zhang
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China
| | - Ji Li
- School of Civil and Environmental Engineering, Harbin Institute of Technology (Shenzhen), Shenzhen 518055, China; Shenzhen Key Laboratory of Water Resource Application and Environmental Pollution Control, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen 518055, China; State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, China.
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8
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Chon NL, Schultz NJ, Zheng H, Lin H. Anion Pathways in the NarK Nitrate/Nitrite Exchanger. J Chem Inf Model 2023; 63:5142-5152. [PMID: 37585651 PMCID: PMC10482320 DOI: 10.1021/acs.jcim.3c00295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Indexed: 08/18/2023]
Abstract
NarK nitrate/nitrite antiporter imports nitrate (a mineral form of the essential element nitrogen) into the cell and exports nitrite (a metabolite that can be toxic in high concentrations) out of the cell. However, many details about its operational mechanism remain poorly understood. In this work, we performed steered molecular dynamics simulations of anion translocations and quantum-chemistry model calculations of the binding sites to study the wild-type NarK protein and its R89K mutant. Our results shed light on the importance of the two strictly conserved binding-site arginine residues (R89 and R305) and two glycine-rich signature motifs (G164-M176 and G408-F419) in anion movement through the pore. We also observe conformational changes of the protein during anion migration. For the R89K mutant, our quantum calculations reveal a competition for a proton between the anion (especially nitrite) and lysine, which can potentially slow down or even trap the anion in the pore. Our findings provide a possible explanation for the striking experimental finding that the arginine-to-lysine mutation, despite preserving the charge, impedes or abolishes anion transport in such mutants of NarK and other similar nitrate/nitrite exchangers.
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Affiliation(s)
- Nara Lee Chon
- Department
of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Natalie Jean Schultz
- Department
of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
| | - Hongjin Zheng
- Department
of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Hai Lin
- Department
of Chemistry, University of Colorado Denver, Denver, Colorado 80217, United States
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9
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Hamada MA, Soliman ERS. Characterization and genomics identification of key genes involved in denitrification-DNRA-nitrification pathway of plant growth-promoting rhizobacteria (Serratia marcescens OK482790). BMC Microbiol 2023; 23:210. [PMID: 37543572 PMCID: PMC10403818 DOI: 10.1186/s12866-023-02941-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/11/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND A wide variety of microorganisms, including bacteria, live in the rhizosphere zone of plants and have an impact on plant development both favorably and adversely. The beneficial outcome is due to the presence of rhizobacteria that promote plant growth (PGPR). RESULTS In this study, a bacterial strain was isolated from lupin rhizosphere and identified genetically as Serratia marcescens (OK482790). Several biochemically and genetically characteristics were confirmed in vitro and in vivo to determine the OK482790 strain ability to be PGPR. The in vitro results revealed production of different lytic enzymes (protease, lipase, cellulase, and catalase), antimicrobial compounds (hydrogen cyanide, and siderophores), ammonia, nitrite, and nitrate and its ability to reduce nitrate to nitrite. In silico and in vitro screening proposed possible denitrification-DNRA-nitrification pathway for OK482790 strain. The genome screening indicated the presence of nitrite and nitrate genes encoding Nar membrane bound sensor proteins (NarK, NarQ and NarX). Nitrate and nitrite reductase encoding genes (NarI, NarJ, NarH, NarG and NapC/NirT) and (NirB, NirC, and NirD) are also found in addition to nitroreductases (NTR) and several oxidoreductases. In vivo results on wheat seedlings confirmed that seedlings growth was significantly improved by soil inoculation of OK482790 strain. CONCLUSIONS This study provides evidence for participation of S. marcescens OK482790 in nitrogen cycling via the denitrification-DNRA-nitrification pathway and for its ability to produce several enzymes and compounds that support the beneficial role of plant-microbe interactions to sustain plant growth and development for a safer environment.
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Affiliation(s)
- Marwa A Hamada
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt
| | - Elham R S Soliman
- Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt.
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Yu L, Ju CJ, Jing KY, Wang ZY, Niyazi S, Wang Q. The role of anthraquinone-2-sulfonate on intra/extracellular electron transfer of anaerobic nitrate reduction. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 333:117455. [PMID: 36758409 DOI: 10.1016/j.jenvman.2023.117455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
To improve the electron (e-) transfer efficiency, exogenous redox mediators (RMs) were usually employed to enhance the denitrification efficiency due to the electron shuttling. Previous studies were mainly focused on how to improve the extracellular electron transfer (EET) by exogenous RMs. However, the intracellular electron transfer (IET), another crucial e- transfer pathway, of biological denitrification was scarcely reported, especially for the relationship between the denitrification and IET. In this study, Coenzyme Q, Complexes I, II and III were determined as the core components in the IET chain of denitrification by using four specific respiration chain inhibitors (RCIs). Anthraquinone-2-sulfonate (AQS) partially recovered the IET of denitrification from NO3--N to N2 gas when the RCIs were added. Specifically, the generations of N2 gas were improved by 9.68%-18.25% in the experiments with RCIs and AQS, comparing to that with RCIs. nrfA gene was not detected by reverse transcription-polymerase chain reaction, suggesting that Klebsiella oxytoca strain could not conduct dissimilatory nitrate reduction to ammonium. Nitrate assimilation was considered as the main NH4+-N formation way of K. oxytoca strain. The two e- transfer pathways of denitrification were constructed and the roles of AQS on the IET and EET of denitrification were specifically discussed. The results of this study provided a better understanding of the e- transfer pathways of denitrification, and suggested a potential practical use of exogenous RM on bio-treatment of nitrate-containing wastewater.
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Affiliation(s)
- Lei Yu
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
| | - Cheng-Jia Ju
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Kai-Yan Jing
- College of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Zi-Yang Wang
- Soil Environment Research Institute, Jiangsu Provincial Academy of Environmental Science, 210003, Nanjing, China
| | - Shareen Niyazi
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
| | - Quan Wang
- Department of Environmental Engineering, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China; College of Biology and the Environment, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China.
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11
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Sauve S, Williamson J, Polasa A, Moradi M. Ins and Outs of Rocker Switch Mechanism in Major Facilitator Superfamily of Transporters. MEMBRANES 2023; 13:membranes13050462. [PMID: 37233523 DOI: 10.3390/membranes13050462] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/27/2023]
Abstract
The major facilitator superfamily (MFS) of transporters consists of three classes of membrane transporters: symporters, uniporters, and antiporters. Despite such diverse functions, MFS transporters are believed to undergo similar conformational changes within their distinct transport cycles, known as the rocker-switch mechanism. While the similarities between conformational changes are noteworthy, the differences are also important since they could potentially explain the distinct functions of symporters, uniporters, and antiporters of the MFS superfamily. We reviewed a variety of experimental and computational structural data on a select number of antiporters, symporters, and uniporters from the MFS family to compare the similarities and differences of the conformational dynamics of three different classes of transporters.
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Affiliation(s)
- Stephanie Sauve
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Joseph Williamson
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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12
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Jaunet-Lahary T, Shimamura T, Hayashi M, Nomura N, Hirasawa K, Shimizu T, Yamashita M, Tsutsumi N, Suehiro Y, Kojima K, Sudo Y, Tamura T, Iwanari H, Hamakubo T, Iwata S, Okazaki KI, Hirai T, Yamashita A. Structure and mechanism of oxalate transporter OxlT in an oxalate-degrading bacterium in the gut microbiota. Nat Commun 2023; 14:1730. [PMID: 37012268 PMCID: PMC10070484 DOI: 10.1038/s41467-023-36883-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 02/20/2023] [Indexed: 04/05/2023] Open
Abstract
An oxalate-degrading bacterium in the gut microbiota absorbs food-derived oxalate to use this as a carbon and energy source, thereby reducing the risk of kidney stone formation in host animals. The bacterial oxalate transporter OxlT selectively uptakes oxalate from the gut to bacterial cells with a strict discrimination from other nutrient carboxylates. Here, we present crystal structures of oxalate-bound and ligand-free OxlT in two distinct conformations, occluded and outward-facing states. The ligand-binding pocket contains basic residues that form salt bridges with oxalate while preventing the conformational switch to the occluded state without an acidic substrate. The occluded pocket can accommodate oxalate but not larger dicarboxylates, such as metabolic intermediates. The permeation pathways from the pocket are completely blocked by extensive interdomain interactions, which can be opened solely by a flip of a single side chain neighbouring the substrate. This study shows the structural basis underlying metabolic interactions enabling favourable symbiosis.
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Affiliation(s)
- Titouan Jaunet-Lahary
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan
| | - Tatsuro Shimamura
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
| | - Masahiro Hayashi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Norimichi Nomura
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kouta Hirasawa
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | | | | | - Naotaka Tsutsumi
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
- School of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yuta Suehiro
- School of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Keiichi Kojima
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Yuki Sudo
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Takashi Tamura
- Graduate School of Environmental and Life Sciences, Okayama University, Okayama, 700-8530, Japan
| | - Hiroko Iwanari
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - Takao Hamakubo
- Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, 153-8904, Japan
| | - So Iwata
- Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kei-Ichi Okazaki
- Research Center for Computational Science, Institute for Molecular Science, National Institutes of Natural Sciences, Okazaki, 444-8585, Japan.
| | | | - Atsuko Yamashita
- Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
- RIKEN SPring-8 Center, Sayo, 679-5148, Japan.
- School of Pharmaceutical Sciences, Okayama University, Okayama, 700-8530, Japan.
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13
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Zhai G, Zhang Z, Dong C. Mutagenesis and functional analysis of SotB: A multidrug transporter of the major facilitator superfamily from Escherichia coli. Front Microbiol 2022; 13:1024639. [PMID: 36386622 PMCID: PMC9650428 DOI: 10.3389/fmicb.2022.1024639] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/11/2022] [Indexed: 10/28/2023] Open
Abstract
Dysfunction of the major facilitator superfamily multidrug (MFS Mdr) transporters can lead to a variety of serious diseases in human. In bacteria, such membrane proteins are often associated with bacterial resistance. However, as one of the MFS Mdr transporters, the physiological function of SotB from Escherichia coli is poorly understood to date. To better understand the function and mechanism of SotB, a systematic study on this MFS Mdr transporter was carried out. In this study, SotB was found to directly efflux L-arabinose in E. coli by overexpressing sotB gene combined with cell based radiotracer uptake assay. Besides, the surface plasmon resonance (SPR) studies, the L-arabinose inhibition assays, together with precise molecular docking analysis, reveal the following: (i) the functional importance of E29 (protonation), H115/N343 (substrate recognition), and W119/S339 (substrate efflux) in the SotB mediated export of L-arabinose, and (ii) for the first time find that D-xylose, an isomer of L-arabinose, likely hinders the binding of L-arabinose with SotB as a competitive inhibitor. Finally, by analyzing the structure of SotB2 (shares 62.8% sequence similarity with SotB) predicted by AlphaFold 2, the different molecular mechanism of substrate recognition between SotB and SotB2 is explained. To our knowledge, this is the first systematic study of MFS Mdr transporter SotB. The structural information, together with the biochemical inspections in this study, provide a valuable framework for further deciphering the functional mechanisms of the physiologically important L-arabinose transporter SotB and its family.
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Affiliation(s)
| | - Zhengyu Zhang
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
| | - Changjiang Dong
- Department of Endocrinology, Zhongnan Hospital of Wuhan University, School of Pharmaceutical Sciences, Wuhan University, Wuhan, China
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14
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Nitrate Utilization Promotes Systemic Infection of Salmonella Typhimurium in Mice. Int J Mol Sci 2022; 23:ijms23137220. [PMID: 35806223 PMCID: PMC9266322 DOI: 10.3390/ijms23137220] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/07/2023] Open
Abstract
Salmonella Typhimurium is an invasive enteric pathogen that causes gastroenteritis in humans and life-threatening systemic infections in mice. During infection of the intestine, S. Typhimurium can exploit nitrate as an electron acceptor to enhance its growth. However, the roles of nitrate on S. Typhimurium systemic infection are unknown. In this study, nitrate levels were found to be significantly increased in the liver and spleen of mice systemically infected by S. Typhimurium. Mutations in genes encoding nitrate transmembrane transporter (narK) or nitrate-producing flavohemoprotein (hmpA) decreased the replication of S. Typhimurium in macrophages and reduced systemic infection in vivo, suggesting that nitrate utilization promotes S. Typhimurium systemic virulence. Moreover, nitrate utilization contributes to the acidification of the S. Typhimurium cytoplasm, which can sustain the virulence of S. Typhimurium by increasing the transcription of virulence genes encoding on Salmonella pathogenicity island 2 (SPI-2). Furthermore, the growth advantage of S. Typhimurium conferred by nitrate utilization occurred only under low-oxygen conditions, and the nitrate utilization was activated by both the global regulator Fnr and the nitrate-sensing two-component system NarX-NarL. Collectively, this study revealed a novel mechanism adopted by Salmonella to interact with its host and increase its virulence.
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15
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Wang N, Gao J, Wang Q, Xiao S, Zhuang G. Antimicrobial peptide antibiotics inhibit aerobic denitrification via affecting electron transportation and remolding carbon metabolism. JOURNAL OF HAZARDOUS MATERIALS 2022; 431:128616. [PMID: 35359112 DOI: 10.1016/j.jhazmat.2022.128616] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 01/17/2022] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
The harmful effects of antibiotics on biological denitrification have attracted widespread attention due to their excessive usage. Polymyxin B (PMB) as the typical antimicrobial peptides having been regarded as the "last hope" for treatment of multidrug-resistance bacteria, has also been detected in wastewater. However, little is known about the influence of PMB on aerobic denitrification. In this study, the impact of PMB on aerobic denitrification performance was investigated. Results showed 0.50 mg/L PMB decreased nitrate removal efficiency from 97.4% to 85.3%, and drove denitrifiers to transform more nitrate to biomass instead of producing gas-N. The live/dead staining method showed PMB damaged bacterial membrane. Transcriptome analysis further indicated the key enzymes participating in denitrification and aerobic respiratory chains were suppressed by PMB. To resist the PMB stress, denitrifiers formed thicker biofilm to protect cells from PMB damaging and thus remodeling the central carbon metabolism. Further investigation revealed denitrifiers have different preference on various carbon sources when PMB is present. Subsequently, the underlying mechanism of the distinctive carbon sources preference was explored by the combination of transcriptome and metabolism analysis. Overall, our data suggested denitrifiers have distinctive carbon sources preference under PMB treatment conditions, reminding us that carbon source selection should be cautious in practical applications.
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Affiliation(s)
- Na Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Gao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qiuying Wang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujie Xiao
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoqiang Zhuang
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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16
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Wu Z, Han Z, Zhou W, Sun X, Chen L, Yang S, Hu J, Li C. Insight into the Nucleoside Transport and Inhibition of Human ENT1. Curr Res Struct Biol 2022; 4:192-205. [PMID: 35677775 PMCID: PMC9168172 DOI: 10.1016/j.crstbi.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/02/2022] [Accepted: 05/18/2022] [Indexed: 12/03/2022] Open
Abstract
The human equilibrative nucleoside transporter 1 (hENT1) is an effective controller of adenosine signaling by regulating its extracellular and intracellular concentration, and has become a solid drug target of clinical used adenosine reuptake inhibitors (AdoRIs). Currently, the mechanisms of adenosine transport and inhibition for hENT1 remain unclear, which greatly limits the in-depth understanding of its inner workings as well as the development of novel inhibitors. In this work, the dynamic details of hENT1 underlie adenosine transport and the inhibition mechanism of the non-nucleoside AdoRIs dilazep both were investigated by comparative long-time unbiased molecular dynamics simulations. The calculation results show that the conformational transitions of hENT1 from the outward open to metastable occluded state are mainly driven by TM1, TM2, TM7 and TM9. One of the trimethoxyphenyl rings in dilazep serves as the adenosyl moiety of the endogenous adenosine substrate to competitively occupy the orthosteric site of hENT1. Due to extensive and various VDW interactions with N30, M33, M84, P308 and F334, the other trimethoxyphenyl ring is stuck in the opportunistic site near the extracellular side preventing the complete occlusion of thin gate simultaneously. Obviously, dilazep shows significant inhibitory activity by disrupting the local induce-fit action in substrate binding cavity and blocking the transport cycle of whole protein. This study not only reveals the nucleoside transport mechanism by hENT1 at atomic level, but also provides structural guidance for the subsequent design of novel non-nucleoside AdoRIs with enhanced pharmacologic properties. The transitions of hENT1 from the outward open to metastable occluded state are mainly driven by TM1, TM2, TM7 and TM9. The induce-fit action by adenosine recognition precedes. inward contraction of the extracellular side. Dilazep exerts its special hENT1 inhibitory function through competitive binding and allosteric regulation. A gating strategy of extracellular loop is revealed to ensure adenosine is firmly located in the transport cavity.
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Affiliation(s)
- Zhixiang Wu
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Zhongjie Han
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Wenxue Zhou
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Xiaohan Sun
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Lei Chen
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Shuang Yang
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
| | - Jianping Hu
- Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, China
- Corresponding author. Key Laboratory of Medicinal and Edible Plants Resources, Development of Sichuan Education Department, School of Pharmacy, Chengdu University, Chengdu, 610106, China.
| | - Chunhua Li
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
- Corresponding author. Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, 100124, China.
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17
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González D, Robas M, Fernández V, Bárcena M, Probanza A, Jiménez PA. Comparative Metagenomic Study of Rhizospheric and Bulk Mercury-Contaminated Soils in the Mining District of Almadén. Front Microbiol 2022; 13:797444. [PMID: 35330761 PMCID: PMC8940170 DOI: 10.3389/fmicb.2022.797444] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/17/2022] [Indexed: 12/22/2022] Open
Abstract
Soil contamination by heavy metals, particularly mercury (Hg), is a problem that can seriously affect the environment, animals, and human health. Hg has the capacity to biomagnify in the food chain. That fact can lead to pathologies, of those which affect the central nervous system being the most severe. It is convenient to know the biological environmental indicators that alert of the effects of Hg contamination as well as the biological mechanisms that can help in its remediation. To contribute to this knowledge, this study conducted comparative analysis by the use of Shotgun metagenomics of the microbial communities in rhizospheric soils and bulk soil of the mining region of Almadén (Ciudad Real, Spain), one of the most affected areas by Hg in the world The sequences obtained was analyzed with MetaPhlAn2 tool and SUPER-FOCUS. The most abundant taxa in the taxonomic analysis in bulk soil were those of Actinobateria and Alphaproteobacteria. On the contrary, in the rhizospheric soil microorganisms belonging to the phylum Proteobacteria were abundant, evidencing that roots have a selective effect on the rhizospheric communities. In order to analyze possible indicators of biological contamination, a functional potential analysis was performed. The results point to a co-selection of the mechanisms of resistance to Hg and the mechanisms of resistance to antibiotics or other toxic compounds in environments contaminated by Hg. Likewise, the finding of antibiotic resistance mechanisms typical of the human clinic, such as resistance to beta-lactams and glycopeptics (vancomycin), suggests that these environments can behave as reservoirs. The sequences involved in Hg resistance (operon mer and efflux pumps) have a similar abundance in both soil types. However, the response to abiotic stress (salinity, desiccation, and contaminants) is more prevalent in rhizospheric soil. Finally, sequences involved in nitrogen fixation and metabolism and plant growth promotion (PGP genes) were identified, with higher relative abundances in rhizospheric soils. These findings can be the starting point for the targeted search for microorganisms suitable for further use in bioremediation processes in Hg-contaminated environments.
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Affiliation(s)
- Daniel González
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Marina Robas
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Vanesa Fernández
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Marta Bárcena
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Agustín Probanza
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
| | - Pedro A Jiménez
- Department of Pharmaceutical Science and Health, CEU Universities, Boadilla del Monte, Spain
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18
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Mato J, Duster AW, Guidez EB, Lin H. Adaptive-Partitioning Multilayer Dynamics Simulations: 1. On-the-Fly Switch between Two Quantum Levels of Theory. J Chem Theory Comput 2021; 17:5456-5465. [PMID: 34448578 DOI: 10.1021/acs.jctc.1c00556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We propose to generalize the previously developed two-layer permuted adaptive-partitioning quantum-mechanics/molecular-mechanics (QM/MM), which reclassifies atoms as QM or MM on-the-fly in dynamics simulations, to multilayer adaptive-partitioning algorithms that enable multiple levels of theory. In this work, we formulate two new algorithms that smoothly interpolate the energy between two QM (Q1 and Q2) levels of theory. The first "permuted adaptive-partitioning" scheme is based on the weighted many-body expansion of the potential, as in the adaptive-partitioning QM/MM. Unconventional and potentially more efficient, the second "interpolated adaptive-partitioning" method employs alchemical QM calculations with Q1/Q2-mixed basis sets, Fock matrices, and overlap matrices. To our knowledge, this is the first time that such alchemical calculations are performed in QM, although they are routinely done in MM. Test calculations on water-cluster models show that both new algorithms indeed yield smooth energy curves when water molecules shift between Q1 and Q2.
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Affiliation(s)
- Joani Mato
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
| | - Adam W Duster
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
| | - Emilie B Guidez
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
| | - Hai Lin
- Department of Chemistry, University of Colorado, Denver, Denver, Colorado 80217, United States
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19
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Zhou Q, Xie X, Feng F, Huang S, Sun Y. Impact of acyl-homoserine lactones on the response of nitrogen cycling in sediment to florfenicol stress. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 785:147294. [PMID: 33932672 DOI: 10.1016/j.scitotenv.2021.147294] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 04/17/2021] [Accepted: 04/17/2021] [Indexed: 06/12/2023]
Abstract
Antibiotic residuals disrupt environmental microbial metabolism and can alter the nitrogen cycle. Quorum sensing has both inter- and intra-species effects that are directly related to the population densities necessary for microbial nitrogen cycling. Here, we explored how acyl-homoserine lactones (AHLs) can change the response of nitrogen cycling to florfenicol in sediments. AHLs might promote microbial reproduction in sediment under florfenicol stress. The relative abundances of Proteobacteria and Euryarchaeota in the antibiotic and AHL treatment groups were higher than those in the control group. AHLs reduced the effects of antibiotics on the abundance of Nitrospira at sampling times of 3d, 10d, and 20d. In the annotation results, nitrate reductase showed the highest abundance, followed by nitrite reductase, nitrogenase, nitric oxide (NO) reductase, nitrous oxide reductase, and ammonia monooxygenase. The abundances of these genes have changed in response to pressure by florfenicol and the addition of AHLs. We also found significant associations between the nitrogen cycle-related functional genes and dominant genera. In particular, glutamate metabolic enzymes and nitrate/nitrite transporters were the primary participants in correlation. Florfenicol can rapidly alter microbial community structures in sediments, affect the functional diversity of microorganisms, and hinder the nitrogen cycle. The response of microorganisms to florfenicol was regulated by the addition of AHLs. This process might alter the use and production of nitrogenous substances in the environment by functional communities in sediments.
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Affiliation(s)
- Qin Zhou
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China; College of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Xiying Xie
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Fengling Feng
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China
| | - Shujian Huang
- College of Life Sciences and Engineering, Foshan University, Foshan, Guangdong Province, China
| | - Yongxue Sun
- National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, 483 Wushan Road, Guangzhou 510642, China.
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20
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Drew D, North RA, Nagarathinam K, Tanabe M. Structures and General Transport Mechanisms by the Major Facilitator Superfamily (MFS). Chem Rev 2021; 121:5289-5335. [PMID: 33886296 PMCID: PMC8154325 DOI: 10.1021/acs.chemrev.0c00983] [Citation(s) in RCA: 165] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Indexed: 12/12/2022]
Abstract
The major facilitator superfamily (MFS) is the largest known superfamily of secondary active transporters. MFS transporters are responsible for transporting a broad spectrum of substrates, either down their concentration gradient or uphill using the energy stored in the electrochemical gradients. Over the last 10 years, more than a hundred different MFS transporter structures covering close to 40 members have provided an atomic framework for piecing together the molecular basis of their transport cycles. Here, we summarize the remarkable promiscuity of MFS members in terms of substrate recognition and proton coupling as well as the intricate gating mechanisms undergone in achieving substrate translocation. We outline studies that show how residues far from the substrate binding site can be just as important for fine-tuning substrate recognition and specificity as those residues directly coordinating the substrate, and how a number of MFS transporters have evolved to form unique complexes with chaperone and signaling functions. Through a deeper mechanistic description of glucose (GLUT) transporters and multidrug resistance (MDR) antiporters, we outline novel refinements to the rocker-switch alternating-access model, such as a latch mechanism for proton-coupled monosaccharide transport. We emphasize that a full understanding of transport requires an elucidation of MFS transporter dynamics, energy landscapes, and the determination of how rate transitions are modulated by lipids.
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Affiliation(s)
- David Drew
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Rachel A. North
- Department
of Biochemistry and Biophysics, Stockholm
University, SE 106 91 Stockholm, Sweden
| | - Kumar Nagarathinam
- Center
of Structural and Cell Biology in Medicine, Institute of Biochemistry, University of Lübeck, D-23538, Lübeck, Germany
| | - Mikio Tanabe
- Structural
Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), Oho 1-1, Tsukuba, Ibaraki 305-0801, Japan
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21
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Gomaa F, Utter DR, Powers C, Beaudoin DJ, Edgcomb VP, Filipsson HL, Hansel CM, Wankel SD, Zhang Y, Bernhard JM. Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments. SCIENCE ADVANCES 2021; 7:7/22/eabf1586. [PMID: 34039603 PMCID: PMC8153729 DOI: 10.1126/sciadv.abf1586] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 04/05/2021] [Indexed: 05/14/2023]
Abstract
Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom's plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among "typical" eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.
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Affiliation(s)
- Fatma Gomaa
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Daniel R Utter
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Christopher Powers
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - David J Beaudoin
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | | | - Colleen M Hansel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Scott D Wankel
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Ying Zhang
- Department of Cell and Molecular Biology, College of the Environment and Life Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Joan M Bernhard
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
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22
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Feng J, Selvam B, Shukla D. How do antiporters exchange substrates across the cell membrane? An atomic-level description of the complete exchange cycle in NarK. Structure 2021; 29:922-933.e3. [PMID: 33836147 DOI: 10.1016/j.str.2021.03.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 01/07/2021] [Accepted: 03/19/2021] [Indexed: 11/19/2022]
Abstract
Major facilitator superfamily (MFS) proteins operate via three different mechanisms: uniport, symport, and antiport. Despite extensive investigations, the molecular understanding of antiporters is less advanced than that of other transporters due to the complex coupling between two substrates and the lack of distinct structures. We employ extensive all-atom molecular dynamics simulations to dissect the complete substrate exchange cycle of the bacterial NO3-/NO2- antiporter, NarK. We show that paired basic residues in the binding site prevent the closure of unbound protein and ensure the exchange of two substrates. Conformational transition occurs only in the presence of substrate, which weakens the electrostatic repulsion and stabilizes the transporter. Furthermore, we propose a state-dependent substrate exchange model, in which the relative spacing between the paired basic residues determines whether NO3- and NO2- bind simultaneously or sequentially. Overall, this work presents a general working model for the antiport mechanism within the MFS.
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Affiliation(s)
- Jiangyan Feng
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Center for Digital Agriculture, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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23
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Yang J, Feng L, Pi S, Cui D, Ma F, Zhao HP, Li A. A critical review of aerobic denitrification: Insights into the intracellular electron transfer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 731:139080. [PMID: 32417477 DOI: 10.1016/j.scitotenv.2020.139080] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 04/04/2020] [Accepted: 04/26/2020] [Indexed: 05/23/2023]
Abstract
Aerobic denitrification is a novel biological nitrogen removal technology, which has been widely investigated as an alternative to the conventional denitrification and for its unique advantages. To fully comprehend aerobic denitrification, it is essential to clarify the regulatory mechanisms of intracellular electron transfer during aerobic denitrification. However, reports on intracellular electron transfer during aerobic denitrification are rather limited. Thus, the purpose of this review is to discuss the molecular mechanism of aerobic denitrification from the perspective of electron transfer, by summarizing the advancements in current research on electron transfer based on conventional denitrification. Firstly, the implication of aerobic denitrification is briefly discussed, and the status of current research on aerobic denitrification is summarized. Then, the occurring foundation and significance of aerobic denitrification are discussed based on a brief review of the key components involved in the electron transfer of denitrifying enzymes. Moreover, a strategy for enhancing the efficiency of aerobic denitrification is proposed on the basis of the regulatory mechanisms of denitrification enzymes. Finally, scientific outlooks are given for further investigation on aerobic denitrification in the future. This review could help clarify the mechanism of aerobic denitrification from the perspective of electron transfer.
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Affiliation(s)
- Jixian Yang
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Liang Feng
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Shanshan Pi
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - Di Cui
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China; Engineering Research Center for Medicine, College of Pharmacy, Harbin University of Commerce, Harbin 150076, People's Republic of China
| | - Fang Ma
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China
| | - He-Ping Zhao
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, People's Republic of China
| | - Ang Li
- State Key Laboratory of Urban Water Resource and Environment, School of Environment, Harbin Institute of Technology, Harbin 150090, People's Republic of China.
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24
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Wang C, Chao Y, Matera G, Gao Q, Vogel J. The conserved 3' UTR-derived small RNA NarS mediates mRNA crossregulation during nitrate respiration. Nucleic Acids Res 2020; 48:2126-2143. [PMID: 31863581 PMCID: PMC7038943 DOI: 10.1093/nar/gkz1168] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/27/2019] [Accepted: 12/02/2019] [Indexed: 12/13/2022] Open
Abstract
Small noncoding RNAs (sRNAs) from mRNA 3′ UTRs seem to present a previously unrecognized layer of bacterial post-transcriptional control whereby mRNAs influence each other's expression, independently of transcriptional control. Studies in Escherichia coli and Salmonella enterica showed that such sRNAs are natural products of RNase E-mediated mRNA decay and associate with major RNA-binding proteins (RBPs) such as Hfq and ProQ. If so, there must be additional sRNAs from mRNAs that accumulate only under specific physiological conditions. We test this prediction by characterizing candidate NarS that represents the 3′ UTR of nitrate transporter NarK whose gene is silent during standard aerobic growth. We find that NarS acts by Hfq-dependent base pairing to repress the synthesis of the nitrite transporter, NirC, resulting in mRNA cross-regulation of nitrate and nitrite transporter genes. Interestingly, the NarS-mediated repression selectively targets the nirC cistron of the long nirBDC-cysG operon, an observation that we rationalize as a mechanism to protect the bacterial cytoplasm from excessive nitrite toxicity during anaerobic respiration with abundant nitrate. Our successful functional assignment of a 3′ UTR sRNA from a non-standard growth condition supports the notion that mRNA crossregulation is more pervasive than currently appreciated.
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Affiliation(s)
- Chuan Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200033, PR China.,Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Yanjie Chao
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Howard Hughes Medical Institute, Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Gianluca Matera
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200033, PR China
| | - Jörg Vogel
- Institute for Molecular Infection Biology, University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Center for Infection Research (HZI), D-97080 Würzburg, Germany
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25
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Sharma M, Anirudh CR. In silico characterization of residues essential for substrate binding of human cystine transporter, xCT. J Mol Model 2019; 25:336. [PMID: 31705320 DOI: 10.1007/s00894-019-4233-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 10/14/2019] [Indexed: 02/06/2023]
Abstract
xCT is a sodium-independent amino acid antiporter that imports L-cystine and exports L-glutamate in a 1:1 ratio. It is a component of heterodimeric amino acid transporter system Xc- working at the cross-roads of maintaining neurological processes and regulating antioxidant defense. The transporter has 12 transmembrane domains with intracellular N- and C-termini, and like other transporter proteins can undergo various conformational changes while switching the ligand accessibilities from intracellular to extracellular site. In the present study, we generated two homology models of human xCT in two distinct conformations: inward-facing occluded state and outward-facing open state. Our results indicated the substrate translocation channel composed of transmembrane helices TMs 1, 3, 6, 8, and 10. We docked anionic L-cystine and L-glutamate within the cavities to assess the two distinct binding scenarios for xCT as antiporter. We also assessed the interactions between the ligands and transporter and observed that ligands bind to similar residues within the channel. Using MM-PBSA/MM-GBSA approach, we computed the binding energies of these ligands to different conformational states. Cystine and glutamate bind xCT with favorable binding energies, with more favorable binding observed in inward occluded state than in outward open state. We further computed the residue-wise decomposition of these binding energies and identified the residues as essential for substrate binding/permeation. Filtering the residues that form favorable energetic contributions to the ligand binding in both the states, our studies suggest T56, A60, R135, A138, V141, Y244, A247, F250, S330, L392, and R396 as critical residues for ligand binding as well as ligand transport for any conformational state adopted by xCT during its transport cycle. .Graphical Abstract.
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Affiliation(s)
- Monika Sharma
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India.
| | - C R Anirudh
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Sector 81, Knowledge City, SAS, Nagar, Punjab, India
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26
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Structure and Mechanism of the Divalent Anion/Na⁺ Symporter. Int J Mol Sci 2019; 20:ijms20020440. [PMID: 30669552 PMCID: PMC6359215 DOI: 10.3390/ijms20020440] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/14/2019] [Accepted: 01/18/2019] [Indexed: 12/22/2022] Open
Abstract
Integral membrane proteins of the divalent anion/Na⁺ symporter (DASS) family are conserved from bacteria to humans. DASS proteins typically mediate the coupled uptake of Na⁺ ions and dicarboxylate, tricarboxylate, or sulfate. Since the substrates for DASS include key intermediates and regulators of energy metabolism, alterations of DASS function profoundly affect fat storage, energy expenditure and life span. Furthermore, loss-of-function mutations in a human DASS have been associated with neonatal epileptic encephalopathy. More recently, human DASS has also been implicated in the development of liver cancers. Therefore, human DASS proteins are potentially promising pharmacological targets for battling obesity, diabetes, kidney stone, fatty liver, as well as other metabolic and neurological disorders. Despite its clinical relevance, the mechanism by which DASS proteins recognize and transport anionic substrates remains unclear. Recently, the crystal structures of a bacterial DASS and its humanized variant have been published. This article reviews the mechanistic implications of these structures and suggests future work to better understand how the function of DASS can be modulated for potential therapeutic benefit.
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27
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Abstract
Transport of solutes across biological membranes is essential for cellular life. This process is mediated by membrane transport proteins which move nutrients, waste products, certain drugs and ions into and out of cells. Secondary active transporters couple the transport of substrates against their concentration gradients with the transport of other solutes down their concentration gradients. The alternating access model of membrane transporters and the coupling mechanism of secondary active transporters are introduced in this book chapter. Structural studies have identified typical protein folds for transporters that we exemplify by the major facilitator superfamily (MFS) and LeuT folds. Finally, substrate binding and substrate translocation of the transporters LacY of the MFS and AdiC of the amino acid-polyamine-organocation (APC) superfamily are described.
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Affiliation(s)
- Patrick D Bosshart
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland
| | - Dimitrios Fotiadis
- Swiss National Centre of Competence in Research (NCCR) TransCure, Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012, Bern, Switzerland.
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28
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Majou D, Christieans S. Mechanisms of the bactericidal effects of nitrate and nitrite in cured meats. Meat Sci 2018; 145:273-284. [PMID: 30005374 DOI: 10.1016/j.meatsci.2018.06.013] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/20/2022]
Abstract
For cured meat products, nitrite is recognized for its antimicrobial effects against pathogenic bacteria, even though the specific inhibitory mechanisms are not well known. Nitrite contributes to oxidative stress by being the precursor of peroxynitrite (ONOO-), which is the major strong oxidant. Thus, bacterial stress (highly pH-very low partial pressure of oxygen-dependent) is enhanced by the nitrate-nitrite-peroxynitrite system which is also highly pH- and low partial pressure of oxygen-dependent. Nitrite is a hurdle technology which effectiveness depends on several other hurdle technologies including sodium chloride (accelerating the autoxidation of oxymyoglobin and promote peroxynitrite formation), ascorbate (increasing ONOO- synthesis), and Aw. In this environment, certain species are more resistant than others to acidic, oxidative, and nitrative stresses. The most resistant are gram-negative aerobic/facultative anaerobic bacteria (Escherichia coli, Salmonella), and the most fragile are gram-positive anaerobic bacteria (Clostridium botulinum). This position review highlights the major chemical mechanisms involved, the active molecules and their actions on bacterial metabolisms in the meat ecosystem.
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Affiliation(s)
- Didier Majou
- Association pour la Coordination Technique pour l'Industrie Agro-Alimentaire (ACTIA), 16, rue Claude Bernard, 75005 Paris 05, France
| | - Souad Christieans
- Association pour le Développement de l'Industrie de la Viande (ADIV), 10, rue Jacqueline Auriol, 63039 Clermont-Ferrand, France..
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29
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TosR-Mediated Regulation of Adhesins and Biofilm Formation in Uropathogenic Escherichia coli. mSphere 2018; 3:3/3/e00222-18. [PMID: 29769381 PMCID: PMC5956150 DOI: 10.1128/msphere.00222-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 04/23/2018] [Indexed: 02/07/2023] Open
Abstract
Uropathogenic Escherichia coli strains utilize a variety of adherence factors that assist in colonization of the host urinary tract. TosA (type one secretion A) is a nonfimbrial adhesin that is predominately expressed during murine urinary tract infection (UTI), binds to kidney epithelial cells, and promotes survival during invasive infections. The tosRCBDAEF operon encodes the secretory machinery necessary for TosA localization to the E. coli cell surface, as well as the transcriptional regulator TosR. TosR binds upstream of the tos operon and in a concentration-dependent manner either induces or represses tosA expression. TosR is a member of the PapB family of fimbrial regulators that can participate in cross talk between fimbrial operons. TosR also binds upstream of the pap operon and suppresses PapA production. However, the scope of TosR-mediated cross talk is understudied and may be underestimated. To quantify the global effects of TosR-mediated regulation on the E. coli CFT073 genome, we induced expression of tosR, collected mRNA, and performed high-throughput RNA sequencing (RNA-Seq). These findings show that production of TosR affected the expression of genes involved with adhesins, including P, F1C, and Auf fimbriae, nitrate-nitrite transport, microcin secretion, and biofilm formation.IMPORTANCE Uropathogenic E. coli strains cause the majority of UTIs, which are the second most common bacterial infection in humans. During a UTI, bacteria adhere to cells within the urinary tract, using a number of different fimbrial and nonfimbrial adhesins. Biofilms can also develop on the surfaces of catheters, resulting in complications such as blockage. In this work, we further characterized the regulator TosR, which links both adhesin production and biofilm formation and likely plays a crucial function during UTI and disseminated infection.
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30
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Abstract
Bacteria require iron for growth, with only a few reported exceptions. In many environments, iron is a limiting nutrient for growth and high affinity uptake systems play a central role in iron homeostasis. However, iron can also be detrimental to cells when it is present in excess, particularly under aerobic conditions where its participation in Fenton chemistry generates highly reactive hydroxyl radicals. Recent results have revealed a critical role for iron efflux transporters in protecting bacteria from iron intoxication. Systems that efflux iron are widely distributed amongst bacteria and fall into several categories: P1B-type ATPases, cation diffusion facilitator (CDF) proteins, major facilitator superfamily (MFS) proteins, and membrane bound ferritin-like proteins. Here, we review the emerging role of iron export in both iron homeostasis and as part of the adaptive response to oxidative stress.
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Affiliation(s)
- Hualiang Pi
- Department of Microbiology, Cornell University, Ithaca, NY 14853-8101, USA.
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31
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Mechanism of Substrate Translocation in an Alternating Access Transporter. Cell 2017; 169:96-107.e12. [PMID: 28340354 DOI: 10.1016/j.cell.2017.03.010] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 01/15/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
Abstract
Transporters shuttle molecules across cell membranes by alternating among distinct conformational states. Fundamental questions remain about how transporters transition between states and how such structural rearrangements regulate substrate translocation. Here, we capture the translocation process by crystallography and unguided molecular dynamics simulations, providing an atomic-level description of alternating access transport. Simulations of a SWEET-family transporter initiated from an outward-open, glucose-bound structure reported here spontaneously adopt occluded and inward-open conformations. Strikingly, these conformations match crystal structures, including our inward-open structure. Mutagenesis experiments further validate simulation predictions. Our results reveal that state transitions are driven by favorable interactions formed upon closure of extracellular and intracellular "gates" and by an unfavorable transmembrane helix configuration when both gates are closed. This mechanism leads to tight allosteric coupling between gates, preventing them from opening simultaneously. Interestingly, the substrate appears to take a "free ride" across the membrane without causing major structural rearrangements in the transporter.
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32
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Enhancement of antibiotic productions by engineered nitrate utilization in actinomycetes. Appl Microbiol Biotechnol 2017; 101:5341-5352. [DOI: 10.1007/s00253-017-8292-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 10/19/2022]
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33
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Structure and function of the divalent anion/Na + symporter from Vibrio cholerae and a humanized variant. Nat Commun 2017; 8:15009. [PMID: 28436435 PMCID: PMC5413979 DOI: 10.1038/ncomms15009] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 02/20/2017] [Indexed: 01/15/2023] Open
Abstract
Integral membrane proteins of the divalent anion/Na+ symporter (DASS) family translocate dicarboxylate, tricarboxylate or sulphate across cell membranes, typically by utilizing the preexisting Na+ gradient. The molecular determinants for substrate recognition by DASS remain obscure, largely owing to the absence of any substrate-bound DASS structure. Here we present 2.8-Å resolution X-ray structures of VcINDY, a DASS from Vibrio cholerae that catalyses the co-transport of Na+ and succinate. These structures portray the Na+-bound VcINDY in complexes with succinate and citrate, elucidating the binding sites for substrate and two Na+ ions. Furthermore, we report the structures of a humanized variant of VcINDY in complexes with succinate and citrate, which predict how a human citrate-transporting DASS may interact with its bound substrate. Our findings provide insights into metabolite transport by DASS, establishing a molecular basis for future studies on the regulation of this transport process. Divalent anion/Na+ symporter (DASS) transporters move intermediates of the Krebs cycle across the cell membrane. Here the authors present the substrate-bound structures of VcINDY, a DASS from Vibrio cholerae, which provide insights into the underlying transport mechanism.
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34
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Quistgaard EM, Martinez Molledo M, Löw C. Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121. PLoS One 2017; 12:e0173126. [PMID: 28264013 PMCID: PMC5338821 DOI: 10.1371/journal.pone.0173126] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 02/15/2017] [Indexed: 12/03/2022] Open
Abstract
Major facilitator superfamily (MFS) peptide transporters (typically referred to as PepT, POT or PTR transporters) mediate the uptake of di- and tripeptides, and so play an important dietary role in many organisms. In recent years, a better understanding of the molecular basis for this process has emerged, which is in large part due to a steep increase in structural information. Yet, the conformational transitions underlying the transport mechanism are still not fully understood, and additional data is therefore needed. Here we report in detail the detergent screening, crystallization, experimental MIRAS phasing, and refinement of the peptide transporter PepTSt from Streptococcus thermophilus. The space group is P3121, and the protein is crystallized in a monomeric inward facing form. The binding site is likely to be somewhat occluded, as the lobe encompassing transmembrane helices 10 and 11 is markedly bent towards the central pore of the protein, but the extent of this potential occlusion could not be determined due to disorder at the apex of the lobe. Based on structural comparisons with the seven previously determined P212121 and C2221 structures of inward facing PepTSt, the structural flexibility as well as the conformational changes mediating transition between the inward open and inward facing occluded states are discussed. In conclusion, this report improves our understanding of the structure and conformational cycle of PepTSt, and can furthermore serve as a case study, which may aid in supporting future structure determinations of additional MFS transporters or other integral membrane proteins.
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Affiliation(s)
- Esben M. Quistgaard
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Maria Martinez Molledo
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
| | - Christian Löw
- Centre for Structural Systems Biology (CSSB), DESY and European Molecular Biology Laboratory Hamburg, Hamburg, Germany
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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35
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Goddard AD, Bali S, Mavridou DAI, Luque-Almagro VM, Gates AJ, Dolores Roldán M, Newstead S, Richardson DJ, Ferguson SJ. The Paracoccus denitrificans NarK-like nitrate and nitrite transporters-probing nitrate uptake and nitrate/nitrite exchange mechanisms. Mol Microbiol 2016; 103:117-133. [PMID: 27696579 PMCID: PMC5217062 DOI: 10.1111/mmi.13546] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/29/2016] [Indexed: 12/17/2022]
Abstract
Nitrate and nitrite transport across biological membranes is often facilitated by protein transporters that are members of the major facilitator superfamily. Paracoccus denitrificans contains an unusual arrangement whereby two of these transporters, NarK1 and NarK2, are fused into a single protein, NarK, which delivers nitrate to the respiratory nitrate reductase and transfers the product, nitrite, to the periplasm. Our complementation studies, using a mutant lacking the nitrate/proton symporter NasA from the assimilatory nitrate reductase pathway, support that NarK1 functions as a nitrate/proton symporter while NarK2 is a nitrate/nitrite antiporter. Through the same experimental system, we find that Escherichia coli NarK and NarU can complement deletions in both narK and nasA in P. denitrificans, suggesting that, while these proteins are most likely nitrate/nitrite antiporters, they can also act in the net uptake of nitrate. Finally, we argue that primary sequence analysis and structural modelling do not readily explain why NasA, NarK1 and NarK2, as well as other transporters from this protein family, have such different functions, ranging from net nitrate uptake to nitrate/nitrite exchange.
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Affiliation(s)
- Alan D Goddard
- School of Life Sciences, University of Lincoln, Lincoln, LN6 7TS, UK.,School of Life and Health Sciences, Aston University, Birmingham, B4 7ET, UK.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Shilpa Bali
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Despoina A I Mavridou
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, Kensington, London, SW7 2DD, UK
| | - Victor M Luque-Almagro
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Andrew J Gates
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - M Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1a planta, Campus de Rabanales, Córdoba, 14071, Spain
| | - Simon Newstead
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - David J Richardson
- Centre for Molecular and Structural Biochemistry, School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Stuart J Ferguson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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36
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Affiliation(s)
- David Drew
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden;
| | - Olga Boudker
- Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065;
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37
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Sawers RG, Falke D, Fischer M. Oxygen and Nitrate Respiration in Streptomyces coelicolor A3(2). Adv Microb Physiol 2016; 68:1-40. [PMID: 27134020 DOI: 10.1016/bs.ampbs.2016.02.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Streptomyces species belong to the phylum Actinobacteria and can only grow with oxygen as a terminal electron acceptor. Like other members of this phylum, such as corynebacteria and mycobacteria, the aerobic respiratory chain lacks a soluble cytochrome c. It is therefore implicit that direct electron transfer between the cytochrome bc1 and the cytochrome aa3 oxidase complexes occurs. The complex developmental cycle of streptomycetes manifests itself in the production of spores, which germinate in the presence of oxygen into a substrate mycelium that greatly facilitates acquisition of nutrients necessary to support their saprophytic lifestyle in soils. Due to the highly variable oxygen levels in soils, streptomycetes have developed means of surviving long periods of hypoxia or even anaerobiosis but they fail to grow under these conditions. Little to nothing is understood about how they maintain viability under conditions of oxygen limitation. It is assumed that they can utilise a number of different electron acceptors to help them maintain a membrane potential, one of which is nitrate. The model streptomycete remains Streptomyces coelicolor A3(2), and it synthesises three nonredundant respiratory nitrate reductases (Nar). These Nar enzymes are synthesised during different phases of the developmental cycle and they are functional only under oxygen-limiting (<5% oxygen in air) conditions. Nevertheless, the regulation of their synthesis does not appear to be responsive to nitrate and in the case of Nar1, it appears to be developmentally regulated. This review highlights some of the novel aspects of our current, but somewhat limited, knowledge of respiration in these fascinating bacteria.
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Affiliation(s)
- R G Sawers
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany.
| | - D Falke
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
| | - M Fischer
- Institute for Biology/Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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38
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Understanding transport by the major facilitator superfamily (MFS): structures pave the way. Nat Rev Mol Cell Biol 2016; 17:123-32. [PMID: 26758938 DOI: 10.1038/nrm.2015.25] [Citation(s) in RCA: 277] [Impact Index Per Article: 34.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Members of the major facilitator superfamily (MFS) of transport proteins are essential for the movement of a wide range of substrates across biomembranes. As this transport requires a series of conformational changes, structures of MFS transporters captured in different conformational states are needed to decipher the transport mechanism. Recently, a large number of MFS transporter structures have been determined, which has provided us with an unprecedented opportunity to understand general aspects of the transport mechanism. We propose an updated model for the conformational cycle of MFS transporters, the 'clamp-and-switch model', and discuss the role of so-called 'gating residues' and the substrate in modulating these conformational changes.
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An integrated biochemical system for nitrate assimilation and nitric oxide detoxification in Bradyrhizobium japonicum. Biochem J 2015; 473:297-309. [PMID: 26564204 PMCID: PMC4724949 DOI: 10.1042/bj20150880] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/12/2015] [Indexed: 12/17/2022]
Abstract
Rhizobia are recognized to establish N2-fixing symbiotic interactions with legume plants. Bradyrhizobium japonicum, the symbiont of soybeans, can denitrify and grow under free-living conditions with nitrate (NO3 (-)) or nitrite (NO2 (-)) as sole nitrogen source. Unlike related bacteria that assimilate NO3 (-), genes encoding the assimilatory NO3 (-) reductase (nasC) and NO2 (-) reductase (nirA) in B. japonicum are located at distinct chromosomal loci. The nasC gene is located with genes encoding an ABC-type NO3 (-) transporter, a major facilitator family NO3 (-)/NO2 (-) transporter (NarK), flavoprotein (Flp) and single-domain haemoglobin (termed Bjgb). However, nirA clusters with genes for a NO3 (-)/NO2 (-)-responsive regulator (NasS-NasT). In the present study, we demonstrate NasC and NirA are both key for NO3 (-) assimilation and that growth with NO3 (-), but not NO2 (-) requires flp, implying Flp may function as electron donor to NasC. In addition, bjgb and flp encode a nitric oxide (NO) detoxification system that functions to mitigate cytotoxic NO formed as a by-product of NO3 (-) assimilation. Additional experiments reveal NasT is required for NO3 (-)-responsive expression of the narK-bjgb-flp-nasC transcriptional unit and the nirA gene and that NasS is also involved in the regulatory control of this novel bipartite assimilatory NO3 (-)/NO2 (-) reductase pathway.
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40
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Taniguchi R, Kato HE, Font J, Deshpande CN, Wada M, Ito K, Ishitani R, Jormakka M, Nureki O. Outward- and inward-facing structures of a putative bacterial transition-metal transporter with homology to ferroportin. Nat Commun 2015; 6:8545. [PMID: 26461048 PMCID: PMC4633820 DOI: 10.1038/ncomms9545] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/03/2015] [Indexed: 12/21/2022] Open
Abstract
In vertebrates, the iron exporter ferroportin releases Fe2+ from cells into plasma, thereby maintaining iron homeostasis. The transport activity of ferroportin is suppressed by the peptide hormone hepcidin, which exhibits upregulated expression in chronic inflammation, causing iron-restrictive anaemia. However, due to the lack of structural information about ferroportin, the mechanisms of its iron transport and hepcidin-mediated regulation remain largely elusive. Here we report the crystal structures of a putative bacterial homologue of ferroportin, BbFPN, in both the outward- and inward-facing states. Despite undetectable sequence similarity, BbFPN adopts the major facilitator superfamily fold. A comparison of the two structures reveals that BbFPN undergoes an intra-domain conformational rearrangement during the transport cycle. We identify a substrate metal-binding site, based on structural and mutational analyses. Furthermore, the BbFPN structures suggest that a predicted hepcidin-binding site of ferroportin is located within its central cavity. Thus, BbFPN may be a valuable structural model for iron homeostasis regulation by ferroportin. Iron export from vertebrate cells is mediated by ferroportin, which is suppressed by the peptide hormone hepcidin. Taniguchi et al. present crystal structures of a putative bacterial ferroportin homologue in both outward- and inward-facing states, providing insight into its transport mechanism.
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Affiliation(s)
- Reiya Taniguchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Hideaki E Kato
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Josep Font
- Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia.,Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Chandrika N Deshpande
- Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia.,Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Miki Wada
- Technical office, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Koichi Ito
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Japan
| | - Ryuichiro Ishitani
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
| | - Mika Jormakka
- Structural Biology Program, Centenary Institute, Locked Bag 6, Sydney, New South Wales 2042, Australia.,Faculty of Medicine, Central Clinical School, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.,Global Research Cluster, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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41
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Nomura N, Verdon G, Kang HJ, Shimamura T, Nomura Y, Sonoda Y, Hussien SA, Qureshi AA, Coincon M, Sato Y, Abe H, Nakada-Nakura Y, Hino T, Arakawa T, Kusano-Arai O, Iwanari H, Murata T, Kobayashi T, Hamakubo T, Kasahara M, Iwata S, Drew D. Structure and mechanism of the mammalian fructose transporter GLUT5. Nature 2015; 526:397-401. [PMID: 26416735 PMCID: PMC4618315 DOI: 10.1038/nature14909] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 07/14/2015] [Indexed: 02/02/2023]
Abstract
The altered activity of the fructose transporter GLUT5, an isoform of the facilitated-diffusion glucose transporter family, has been linked to disorders such as type 2 diabetes and obesity. GLUT5 is also overexpressed in certain tumor cells and inhibitors are potential drugs for these conditions. Here, we describe the crystal structure of GLUT5 from Rattus norvegicus and Bos taurus in open outward- and open inward-facing conformations, respectively. GLUT5 has a major facilitator superfamily fold like other homologous monosaccharide transporters. Based on a comparison of the inward-facing structures of GLUT5 and human GLUT1, a ubiquitous glucose transporter, we show that a single point mutation is enough to switch the substrate binding preference of GLUT5 from fructose to glucose. A comparison of the substrate-free structures of GLUT5 with occluded substrate-bound structures of XylE suggests that, besides global rocker-switch like re-orientation of the bundles, local asymmetric rearrangements of C-terminal bundle helices TMs 7 and 10 underlie a “gated-pore” transport mechanism in such monosaccharide transporters.
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Affiliation(s)
- Norimichi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Grégory Verdon
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K
| | - Hae Joo Kang
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K
| | - Tatsuro Shimamura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yayoi Nomura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yo Sonoda
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K
| | - Saba Abdul Hussien
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Aziz Abdul Qureshi
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mathieu Coincon
- Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Yumi Sato
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hitomi Abe
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshiko Nakada-Nakura
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Tomoya Hino
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takatoshi Arakawa
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Osamu Kusano-Arai
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Hiroko Iwanari
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Takeshi Murata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Systems and Structural Biology Center, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Takuya Kobayashi
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Takao Hamakubo
- Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Michihiro Kasahara
- Laboratory of Biophysics, School of Medicine, Teikyo University, Hachioji, Tokyo 192-0395, Japan
| | - So Iwata
- Department of Cell Biology, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, ERATO, Iwata Human Receptor Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan.,Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Membrane Protein Laboratory, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, Chilton, Oxfordshire, OX11 0DE, U.K.,Research Complex at Harwell Rutherford, Appleton Laboratory, Harwell, Oxford, Didcot, Oxfordshire, OX11 0FA, U.K.,Systems and Structural Biology Center, RIKEN, 1-7-22 Suehirocho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - David Drew
- Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, U.K.,Centre for Biomembrane Research, Department of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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