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Li J, Li Y, Koide A, Kuang H, Torres VJ, Koide S, Wang DN, Traaseth NJ. Proton-coupled transport mechanism of the efflux pump NorA. Nat Commun 2024; 15:4494. [PMID: 38802368 PMCID: PMC11130294 DOI: 10.1038/s41467-024-48759-3] [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: 11/10/2023] [Accepted: 05/13/2024] [Indexed: 05/29/2024] Open
Abstract
Efflux pump antiporters confer drug resistance to bacteria by coupling proton import with the expulsion of antibiotics from the cytoplasm. Despite efforts there remains a lack of understanding as to how acid/base chemistry drives drug efflux. Here, we uncover the proton-coupling mechanism of the Staphylococcus aureus efflux pump NorA by elucidating structures in various protonation states of two essential acidic residues using cryo-EM. Protonation of Glu222 and Asp307 within the C-terminal domain stabilized the inward-occluded conformation by forming hydrogen bonds between the acidic residues and a single helix within the N-terminal domain responsible for occluding the substrate binding pocket. Remarkably, deprotonation of both Glu222 and Asp307 is needed to release interdomain tethering interactions, leading to opening of the pocket for antibiotic entry. Hence, the two acidic residues serve as a "belt and suspenders" protection mechanism to prevent simultaneous binding of protons and drug that enforce NorA coupling stoichiometry and confer antibiotic resistance.
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Affiliation(s)
- Jianping Li
- Department of Chemistry, New York University, New York, NY, USA
| | - Yan Li
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Huihui Kuang
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Victor J Torres
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
- Antimicrobial-Resistant Pathogens Program, New York University School of Medicine, New York, NY, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, USA.
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2
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Newstead S. Future opportunities in solute carrier structural biology. Nat Struct Mol Biol 2024; 31:587-590. [PMID: 38637662 DOI: 10.1038/s41594-024-01271-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 03/07/2024] [Indexed: 04/20/2024]
Abstract
Solute carriers (SLCs) control the flow of small molecules and ions across biological membranes. Over the last 20 years, the pace of research in SLC biology has accelerated markedly, opening new opportunities to treat metabolic diseases, cancer and neurological disorders. Recently, new families of atypical SLCs, with roles in organelle biology, metabolite signaling and trafficking, have expanded their roles in the cell. This Perspective discusses work leading to current advances and the emerging opportunities to target and modulate SLCs to uncover new biology and treat human disease.
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Affiliation(s)
- Simon Newstead
- Department of Biochemistry, University of Oxford, Oxford, UK.
- The Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
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3
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Zhang L, Wang M, Qi R, Yang Y, Liu Y, Ren N, Feng Z, Liu Q, Cao G, Zong G. A novel major facilitator superfamily-type tripartite efflux system CprABC mediates resistance to polymyxins in Chryseobacterium sp. PL22-22A. Front Microbiol 2024; 15:1346340. [PMID: 38596380 PMCID: PMC11002906 DOI: 10.3389/fmicb.2024.1346340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/08/2024] [Indexed: 04/11/2024] Open
Abstract
Background Polymyxin B (PMB) and polymyxin E (colistin, CST) are polymyxin antibiotics, which are considered last-line therapeutic options against multidrug-resistant Gram-negative bacteria in serious infections. However, there is increasing risk of resistance to antimicrobial drugs. Effective efflux pump inhibitors (EPIs) should be developed to help combat efflux pump-mediated antibiotic resistance. Methods Chryseobacterium sp. PL22-22A was isolated from aquaculture sewage under selection with 8 mg/L PMB, and then its genome was sequenced using Oxford Nanopore and BGISEQ-500 platforms. Cpr (Chryseobacterium Polymyxins Resistance) genes encoding a major facilitator superfamily-type tripartite efflux system, were found in the genome. These genes, and the gene encoding a truncation mutant of CprB from which sequence called CprBc was deleted, were amplified and expressed/co-expressed in Escherichia coli DH5α. Minimum inhibitory concentrations (MICs) of polymyxins toward the various E. coli heterologous expression strains were tested in the presence of 2-128 mg/L PMB or CST. The pumping activity of CprABC was assessed via structural modeling using Discovery Studio 2.0 software. Moreover, the influence on MICs of baicalin, a novel MFS EPI, was determined, and the effect was analyzed based on homology modeling. Results Multidrug-resistant bacterial strain Chryseobacterium sp. PL22-22A was isolated in this work; it has notable resistance to polymyxin, with MICs for PMB and CST of 96 and 128 mg/L, respectively. A novel MFS-type tripartite efflux system, named CprABC, was identified in the genome of Chryseobacterium sp. PL22-22A. Heterologous expression and EPI assays indicated that the CprABC system is responsible for the polymyxin resistance of Chryseobacterium sp. PL22-22A. Structural modeling suggested that this efflux system provides a continuous conduit that runs from the CprB funnel through the CprC porin domain to pump polymyxins out of the cell. A specific C-terminal α-helix, CprBc, has an activation function on polymyxin excretion by CprB. The flavonoid compound baicalin was found to affect the allostery of CprB and/or obstruct the substrate conduit, and thus to inhibit extracellular polymyxin transport by CprABC. Conclusion Novel MFS-type tripartite efflux system CprABC in Chryseobacterium sp. PL22-22A mediates resistance to polymyxins, and baicalin is a promising EPI.
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Affiliation(s)
- Lu Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Miao Wang
- Shandong Fengjin Biopharmaceuticals Co., Ltd., Yantai, China
| | - Rui Qi
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Yilin Yang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Ya Liu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Nianqing Ren
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Zihan Feng
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Qihao Liu
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Guangxiang Cao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
| | - Gongli Zong
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji’nan, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji’nan, China
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. eLife 2024; 12:RP92462. [PMID: 38381130 PMCID: PMC10942615 DOI: 10.7554/elife.92462] [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] [Indexed: 02/22/2024] Open
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of major facilitator superfamily transporters. With a conformation-selective nanobody, we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. The available outward-facing sugar-bound structures showed that the N- and C-terminal residues of the inner barrier contribute to the sugar selectivity. The inward-open conformation shows that the sugar selectivity pocket is also broken when the inner barrier is broken. Isothermal titration calorimetry measurements revealed that this inward-facing conformation trapped by this nanobody exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is supported by molecular dynamics simulations. Furthermore, the hydron/deuterium exchange mass spectrometry analyses allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Yuqi Shi
- Thermo Fisher ScientificSan JoseUnited States
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Katleen Willibal
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Nathan D Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator LaboratoryMenlo ParkUnited States
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
| | - Els Pardon
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - H Ronald Kaback
- Department of Physiology, University of California, Los AngelesLos AngelesUnited States
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech UniversityLubbockUnited States
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, VIB, Pleinlaan 2BrusselsBelgium
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2BrusselsBelgium
| | - Rosa Viner
- Thermo Fisher ScientificSan JoseUnited States
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of MedicineLubbockUnited States
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Gao W, Li C, Wang F, Yang Y, Zhang L, Wang Z, Chen X, Tan M, Cao G, Zong G. An efflux pump in genomic island GI-M202a mediates the transfer of polymyxin B resistance in Pandoraea pnomenusa M202. Int Microbiol 2024; 27:277-290. [PMID: 37316617 PMCID: PMC10266961 DOI: 10.1007/s10123-023-00384-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 05/19/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Polymyxin B is considered a last-line therapeutic option against multidrug-resistant gram-negative bacteria, especially in COVID-19 coinfections or other serious infections. However, the risk of antimicrobial resistance and its spread to the environment should be brought to the forefront. METHODS Pandoraea pnomenusa M202 was isolated under selection with 8 mg/L polymyxin B from hospital sewage and then was sequenced by the PacBio RS II and Illumina HiSeq 4000 platforms. Mating experiments were performed to evaluate the transfer of the major facilitator superfamily (MFS) transporter in genomic islands (GIs) to Escherichia coli 25DN. The recombinant E. coli strain Mrc-3 harboring MFS transporter encoding gene FKQ53_RS21695 was also constructed. The influence of efflux pump inhibitors (EPIs) on MICs was determined. The mechanism of polymyxin B excretion mediated by FKQ53_RS21695 was investigated by Discovery Studio 2.0 based on homology modeling. RESULTS The MIC of polymyxin B for the multidrug-resistant bacterial strain P. pnomenusa M202, isolated from hospital sewage, was 96 mg/L. GI-M202a, harboring an MFS transporter-encoding gene and conjugative transfer protein-encoding genes of the type IV secretion system, was identified in P. pnomenusa M202. The mating experiment between M202 and E. coli 25DN reflected the transferability of polymyxin B resistance via GI-M202a. EPI and heterogeneous expression assays also suggested that the MFS transporter gene FKQ53_RS21695 in GI-M202a was responsible for polymyxin B resistance. Molecular docking revealed that the polymyxin B fatty acyl group inserts into the hydrophobic region of the transmembrane core with Pi-alkyl and unfavorable bump interactions, and then polymyxin B rotates around Tyr43 to externally display the peptide group during the efflux process, accompanied by an inward-to-outward conformational change in the MFS transporter. Additionally, verapamil and CCCP exhibited significant inhibition via competition for binding sites. CONCLUSIONS These findings demonstrated that GI-M202a along with the MFS transporter FKQ53_RS21695 in P. pnomenusa M202 could mediate the transmission of polymyxin B resistance.
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Affiliation(s)
- Wenhui Gao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Congcong Li
- Shandong Quancheng Test & Technology Limited Company, Ji'nan, 250101, China
| | - Fengtian Wang
- Jinan Municipal Minzu Hospital, Ji'nan, 250012, China
| | - Yilin Yang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Lu Zhang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China
| | - Zhongxue Wang
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Xi Chen
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Meixia Tan
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China
| | - Guangxiang Cao
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China.
| | - Gongli Zong
- First Affiliated Hospital of Shandong First Medical University, Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, 250117, China.
- NHC Key Laboratory of Biotechnology Drugs (Shandong Academy of Medical Sciences), Ji'nan, 250117, Shandong, China.
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Roy RK, Patra N. Probing the pH Sensitivity of OprM: Insights into Metastable States and Semi-Open Conformation. J Phys Chem B 2024; 128:622-634. [PMID: 38047375 DOI: 10.1021/acs.jpcb.3c05384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Efflux pumps are specialized transport proteins that play a key role in the bacterial defense against a wide spectrum of antibiotics. Hence, understanding the biophysical mechanism associated with this complex system of drug expulsion becomes crucial. This work deals with some vital aspects of the outer membrane factor (OMF) of MexAB-OprM. After being passed through MexB and MexA, efflux substrates have to go through OprM for their final judgment. Thus, it is very important to understand the periplasmic pore opening mechanism and the associated biophysical changes during this process. Our study captures a detailed analysis of the pore opening mechanism involving OprM. With powerful molecular dynamics (MD) techniques such as well-tempered metadynamics, the presence of metastable states in between open and closed states was confirmed. Also, upon mutating R376, the energy barrier for the conversion of the close to open conformation decreases, indicating an important role played by the residue. Further, constant pH MD was performed to capture the effect of pH in both conformations. OprM exhibits distinct conformational states at pH values greater than 5.5 and lower than 5.5, suggesting its pH-responsive characteristics. Overall, our study elucidates a crucial undertaking toward discovering potential inhibitors for MexAB-OprM efflux pumps.
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Affiliation(s)
- Rakesh Kumar Roy
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
| | - Niladri Patra
- Department of Chemistry and Chemical Biology, Indian Institute of Technology (ISM) Dhanbad, Dhanbad 826004, India
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7
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Kim JH, Mailloux L, Bloor D, Maddox B, Humble J. The role of salt bridge networks in the stability of the yeast hexose transporter 1. Biochim Biophys Acta Gen Subj 2023; 1867:130490. [PMID: 37844739 DOI: 10.1016/j.bbagen.2023.130490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/06/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023]
Abstract
BACKGROUND The yeast S. cerevisiae preferably metabolizes glucose through aerobic glycolysis. Glucose transport is facilitated by multiple hexose transporters (Hxts), and their expression and activity are tightly regulated by multiple mechanisms. However, detailed structural and functional analyses of Hxts remain limited, largely due to the lack of crystal structure. METHODS Homology modeling was used to build a 3D structural model for the yeast glucose transporter Hxt1 and investigate the effects of site directed mutations on Hxt1 stability and glucose transport activity. RESULTS The conserved salt bridge-forming residues observed in the human Glut4 and the yeast glucose receptor Rgt2 were identified within and between the two 6-transmembrane spanning segments of Hxt1. Most of the RGT2 mutations that disrupt the salt bridge networks were known to cause constitutive signal generation, whereas the corresponding substitutions in HXT1 were shown to decrease Hxt1 stability. While substitutions of the two residues in the salt bridge 2 in Glut4-E329Q and E393D-were reported to abolish glucose transport, the equivalent substitutions in Hxt1 (D382Q and E454D) did not affect Hxt1 glucose transport activity. CONCLUSIONS Substitutions of equivalent salt bridge-forming residues in Hxt1, Rgt2, and Glut4 are predicted to lock them in an inward-facing conformation but lead to different functional consequences. GENERAL SIGNIFICANCE The salt bridge networks in yeast and human glucose transporters and yeast glucose receptors may play different roles in maintaining their structural and functional integrity.
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Affiliation(s)
- Jeong-Ho Kim
- Department of Biology and Chemistry, Liberty University, 1971 University Blvd, Lynchburg, VA 24502, USA.
| | - Levi Mailloux
- Department of Biology and Chemistry, Liberty University, 1971 University Blvd, Lynchburg, VA 24502, USA
| | - Daniel Bloor
- Department of Biology and Chemistry, Liberty University, 1971 University Blvd, Lynchburg, VA 24502, USA
| | - Bradley Maddox
- Department of Biology and Chemistry, Liberty University, 1971 University Blvd, Lynchburg, VA 24502, USA
| | - Julia Humble
- Department of Biology and Chemistry, Liberty University, 1971 University Blvd, Lynchburg, VA 24502, USA
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8
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Hariharan P, Shi Y, Katsube S, Willibal K, Burrows ND, Mitchell P, Bakhtiiari A, Stanfield S, Pardon E, Kaback HR, Liang R, Steyaert J, Viner R, Guan L. Mobile barrier mechanisms for Na +-coupled symport in an MFS sugar transporter. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558283. [PMID: 37790566 PMCID: PMC10542114 DOI: 10.1101/2023.09.18.558283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
While many 3D structures of cation-coupled transporters have been determined, the mechanistic details governing the obligatory coupling and functional regulations still remain elusive. The bacterial melibiose transporter (MelB) is a prototype of the Na+-coupled major facilitator superfamily transporters. With a conformational nanobody (Nb), we determined a low-sugar affinity inward-facing Na+-bound cryoEM structure. Collectively with the available outward-facing sugar-bound structures, both the outer and inner barriers were localized. The N- and C-terminal residues of the inner barrier contribute to the sugar selectivity pocket. When the inner barrier is broken as shown in the inward-open conformation, the sugar selectivity pocket is also broken. The binding assays by isothermal titration calorimetry revealed that this inward-facing conformation trapped by the conformation-selective Nb exhibited a greatly decreased sugar-binding affinity, suggesting the mechanisms for the substrate intracellular release and accumulation. While the inner/outer barrier shift directly regulates the sugar-binding affinity, it has little or no effect on the cation binding, which is also supported by molecular dynamics simulations. Furthermore, the use of this Nb in combination with the hydron/deuterium exchange mass spectrometry allowed us to identify dynamic regions; some regions are involved in the functionally important inner barrier-specific salt-bridge network, which indicates their critical roles in the barrier switching mechanisms for transport. These complementary results provided structural and dynamic insights into the mobile barrier mechanism for cation-coupled symport.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Yuqi Shi
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Satoshi Katsube
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | | | - Nathan D. Burrows
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Patrick Mitchell
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Light Source, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | | | - Samantha Stanfield
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
| | - Els Pardon
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - H. Ronald Kaback
- Department of Physiology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409, USA
| | - Jan Steyaert
- VIB-VUB Center for Structural Biology, 1050 Brussel, Belgium
| | - Rosa Viner
- Thermo Fisher Scientific, San Jose, CA 95134, USA
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, TX 79424, USA
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9
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Tonduru AK, Maljaei SH, Adla SK, Anamea L, Tampio J, Králová A, Jalkanen AJ, Espada C, Santos IF, Montaser AB, Rautio J, Kronenberger T, Poso A, Huttunen KM. Targeting Glial Cells by Organic Anion-Transporting Polypeptide 1C1 (OATP1C1)-Utilizing l-Thyroxine-Derived Prodrugs. J Med Chem 2023; 66:15094-15114. [PMID: 37930268 PMCID: PMC10683023 DOI: 10.1021/acs.jmedchem.3c01026] [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: 06/08/2023] [Revised: 10/20/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
OATP1C1 (organic anion-transporting polypeptide 1C1) transports thyroid hormones, particularly thyroxine (T4), into human astrocytes. In this study, we investigated the potential of utilizing OATP1C1 to improve the delivery of anti-inflammatory drugs into glial cells. We designed and synthesized eight novel prodrugs by incorporating T4 and 3,5-diiodo-l-tyrosine (DIT) as promoieties to selected anti-inflammatory drugs. The prodrug uptake in OATP1C1-expressing human U-87MG glioma cells demonstrated higher accumulation with T4 promoiety compared to those with DIT promoiety or the parent drugs themselves. In silico models of OATP1C1 suggested dynamic binding for the prodrugs, wherein the pose changed from vertical to horizontal. The predicted binding energies correlated with the transport profiles, with T4 derivatives exhibiting higher binding energies when compared to prodrugs with a DIT promoiety. Interestingly, the prodrugs also showed utilization of oatp1a4/1a5/1a6 in mouse primary astrocytes, which was further supported by docking studies and a great potential for improved brain drug delivery.
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Affiliation(s)
- Arun Kumar Tonduru
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Seyed Hamed Maljaei
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Santosh Kumar Adla
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Landry Anamea
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Janne Tampio
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Adéla Králová
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Aaro J. Jalkanen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Catarina Espada
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Inês Falcato Santos
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Ahmed B. Montaser
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Jarkko Rautio
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
| | - Thales Kronenberger
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
- Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
- Tuebingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
| | - Antti Poso
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
- Department
of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical
Sciences, Eberhard-Karls-Universität, Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
- Tuebingen
Center for Academic Drug Discovery & Development (TüCAD2), 72076 Tuebingen, Germany
- Department
of Internal Medicine VIII, University Hospital
Tübingen, DE 72076 Tübingen, Germany
- Cluster
of Excellence iFIT (EXC 2180) “Image-Guided and Functionally
Instructed Tumor Therapies”, University
of Tübingen, 72076 Tübingen, Germany
| | - Kristiina M. Huttunen
- School
of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, P.O. Box 1627, 70211 Kuopio, Finland
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10
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Deng S, Kim J, Pomraning KR, Gao Y, Evans JE, Hofstad BA, Dai Z, Webb-Robertson BJ, Powell SM, Novikova IV, Munoz N, Kim YM, Swita M, Robles AL, Lemmon T, Duong RD, Nicora C, Burnum-Johnson KE, Magnuson J. Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus. Metab Eng 2023; 80:163-172. [PMID: 37778408 DOI: 10.1016/j.ymben.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/25/2023] [Accepted: 09/18/2023] [Indexed: 10/03/2023]
Abstract
Aconitic acid is an unsaturated tricarboxylic acid that is attractive for its potential use in manufacturing biodegradable and biocompatible polymers, plasticizers, and surfactants. Previously Aspergillus pseudoterreus was engineered as a platform to produce aconitic acid by deleting the cadA (cis-aconitic acid decarboxylase) gene in the itaconic acid biosynthetic pathway. In this study, the aconitic acid transporter gene (aexA) was identified using comparative global discovery proteomics analysis between the wild-type and cadA deletion strains. The protein AexA belongs to the Major Facilitator Superfamily (MFS). Deletion of aexA almost abolished aconitic acid secretion, while its overexpression led to a significant increase in aconitic acid production. Transportation of aconitic acid across the plasma membrane is a key limiting step in its production. In vitro, proteoliposome transport assay further validated AexA's function and substrate specificity. This research provides new approaches to efficiently pinpoint and characterize exporters of fungal organic acids and accelerate metabolic engineering to improve secretion capability and lower the cost of bioproduction.
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Affiliation(s)
- Shuang Deng
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Joonhoon Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kyle R Pomraning
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Yuqian Gao
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - James E Evans
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Beth A Hofstad
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ziyu Dai
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Bobbie-Jo Webb-Robertson
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Samantha M Powell
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Irina V Novikova
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Nathalie Munoz
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Young-Mo Kim
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Marie Swita
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Ana L Robles
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Teresa Lemmon
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Rylan D Duong
- Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Carrie Nicora
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Kristin E Burnum-Johnson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
| | - Jon Magnuson
- DOE Agile Biofoundry, Emeryville, CA, 94608, USA; Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
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11
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Varela MF, Ortiz-Alegria A, Lekshmi M, Stephen J, Kumar S. Functional Roles of the Conserved Amino Acid Sequence Motif C, the Antiporter Motif, in Membrane Transporters of the Major Facilitator Superfamily. BIOLOGY 2023; 12:1336. [PMID: 37887046 PMCID: PMC10604125 DOI: 10.3390/biology12101336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023]
Abstract
The biological membrane surrounding all living cells forms a hydrophobic barrier to the passage of biologically important molecules. Integral membrane proteins called transporters circumvent the cellular barrier and transport molecules across the cell membrane. These molecular transporters enable the uptake and exit of molecules for cell growth and homeostasis. One important collection of related transporters is the major facilitator superfamily (MFS). This large group of proteins harbors passive and secondary active transporters. The transporters of the MFS consist of uniporters, symporters, and antiporters, which share similarities in structures, predicted mechanism of transport, and highly conserved amino acid sequence motifs. In particular, the antiporter motif, called motif C, is found primarily in antiporters of the MFS. The antiporter motif's molecular elements mediate conformational changes and other molecular physiological roles during substrate transport across the membrane. This review article traces the history of the antiporter motif. It summarizes the physiological evidence reported that supports these biological roles.
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Affiliation(s)
- Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA;
| | - Anely Ortiz-Alegria
- Department of Biology, Eastern New Mexico University, Portales, NM 88130, USA;
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
| | - Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
| | - Sanath Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (M.L.); (J.S.); (S.K.)
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12
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Tang H, Li H, Prakaash D, Pedebos C, Qiu X, Sauer DB, Khalid S, Duerr K, Robinson CV. The solute carrier SPNS2 recruits PI(4,5)P 2 to synergistically regulate transport of sphingosine-1-phosphate. Mol Cell 2023; 83:2739-2752.e5. [PMID: 37499662 PMCID: PMC10790328 DOI: 10.1016/j.molcel.2023.06.033] [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: 11/30/2022] [Revised: 05/11/2023] [Accepted: 06/26/2023] [Indexed: 07/29/2023]
Abstract
Solute carrier spinster homolog 2 (SPNS2), one of only four known major facilitator superfamily (MFS) lysolipid transporters in humans, exports sphingosine-1-phosphate (S1P) across cell membranes. Here, we explore the synergistic effects of lipid binding and conformational dynamics on SPNS2's transport mechanism. Using mass spectrometry, we discovered that SPNS2 interacts preferentially with PI(4,5)P2. Together with functional studies and molecular dynamics (MD) simulations, we identified potential PI(4,5)P2 binding sites. Mutagenesis of proposed lipid binding sites and inhibition of PI(4,5)P2 synthesis reduce S1P transport, whereas the absence of the N terminus renders the transporter essentially inactive. Probing the conformational dynamics of SPNS2, we show how synergistic binding of PI(4,5)P2 and S1P facilitates transport, increases dynamics of the extracellular gate, and stabilizes the intracellular gate. Given that SPNS2 transports a key signaling lipid, our results have implications for therapeutic targeting and also illustrate a regulatory mechanism for MFS transporters.
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Affiliation(s)
- Haiping Tang
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - Huanyu Li
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Dheeraj Prakaash
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Conrado Pedebos
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Xingyu Qiu
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK
| | - David B Sauer
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Syma Khalid
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Katharina Duerr
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK; OMass Therapeutics, Ltd., Oxford OX4 2GX, UK
| | - Carol V Robinson
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; Kavli Institute for Nanoscience Discovery, Oxford OX1 3QU, UK.
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13
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Ray S, Gaudet R. Structures and coordination chemistry of transporters involved in manganese and iron homeostasis. Biochem Soc Trans 2023; 51:897-923. [PMID: 37283482 PMCID: PMC10330786 DOI: 10.1042/bst20210699] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/08/2023]
Abstract
A repertoire of transporters plays a crucial role in maintaining homeostasis of biologically essential transition metals, manganese, and iron, thus ensuring cell viability. Elucidating the structure and function of many of these transporters has provided substantial understanding into how these proteins help maintain the optimal cellular concentrations of these metals. In particular, recent high-resolution structures of several transporters bound to different metals enable an examination of how the coordination chemistry of metal ion-protein complexes can help us understand metal selectivity and specificity. In this review, we first provide a comprehensive list of both specific and broad-based transporters that contribute to cellular homeostasis of manganese (Mn2+) and iron (Fe2+ and Fe3+) in bacteria, plants, fungi, and animals. Furthermore, we explore the metal-binding sites of the available high-resolution metal-bound transporter structures (Nramps, ABC transporters, P-type ATPase) and provide a detailed analysis of their coordination spheres (ligands, bond lengths, bond angles, and overall geometry and coordination number). Combining this information with the measured binding affinity of the transporters towards different metals sheds light into the molecular basis of substrate selectivity and transport. Moreover, comparison of the transporters with some metal scavenging and storage proteins, which bind metal with high affinity, reveal how the coordination geometry and affinity trends reflect the biological role of individual proteins involved in the homeostasis of these essential transition metals.
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Affiliation(s)
- Shamayeeta Ray
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
| | - Rachelle Gaudet
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, U.S.A
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14
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Varela MF, Stephen J, Bharti D, Lekshmi M, Kumar S. Inhibition of Multidrug Efflux Pumps Belonging to the Major Facilitator Superfamily in Bacterial Pathogens. Biomedicines 2023; 11:1448. [PMID: 37239119 PMCID: PMC10216197 DOI: 10.3390/biomedicines11051448] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Bacterial pathogens resistant to multiple structurally distinct antimicrobial agents are causative agents of infectious disease, and they thus constitute a serious concern for public health. Of the various bacterial mechanisms for antimicrobial resistance, active efflux is a well-known system that extrudes clinically relevant antimicrobial agents, rendering specific pathogens recalcitrant to the growth-inhibitory effects of multiple drugs. In particular, multidrug efflux pump members of the major facilitator superfamily constitute central resistance systems in bacterial pathogens. This review article addresses the recent efforts to modulate these antimicrobial efflux transporters from a molecular perspective. Such investigations can potentially restore the clinical efficacy of infectious disease chemotherapy.
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Affiliation(s)
- Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM 88130, USA
| | - Jerusha Stephen
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Deeksha Bharti
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Manjusha Lekshmi
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
| | - Sanath Kumar
- ICAR-Central Institute of Fisheries Education (CIFE), Mumbai 400061, India; (J.S.); (D.B.); (M.L.); (S.K.)
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15
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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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16
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Zhou W, Simic P, Zhou IY, Caravan P, Vela Parada X, Wen D, Washington OL, Shvedova M, Pierce KA, Clish CB, Mannstadt M, Kobayashi T, Wein MN, Jüppner H, Rhee EP. Kidney glycolysis serves as a mammalian phosphate sensor that maintains phosphate homeostasis. J Clin Invest 2023; 133:e164610. [PMID: 36821389 PMCID: PMC10104895 DOI: 10.1172/jci164610] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 02/21/2023] [Indexed: 02/24/2023] Open
Abstract
How phosphate levels are detected in mammals is unknown. The bone-derived hormone fibroblast growth factor 23 (FGF23) lowers blood phosphate levels by reducing kidney phosphate reabsorption and 1,25(OH)2D production, but phosphate does not directly stimulate bone FGF23 expression. Using PET scanning and LC-MS, we found that phosphate increases kidney-specific glycolysis and synthesis of glycerol-3-phosphate (G-3-P), which then circulates to bone to trigger FGF23 production. Further, we found that G-3-P dehydrogenase 1 (Gpd1), a cytosolic enzyme that synthesizes G-3-P and oxidizes NADH to NAD+, is required for phosphate-stimulated G-3-P and FGF23 production and prevention of hyperphosphatemia. In proximal tubule cells, we found that phosphate availability is substrate-limiting for glycolysis and G-3-P production and that increased glycolysis and Gpd1 activity are coupled through cytosolic NAD+ recycling. Finally, we show that the type II sodium-dependent phosphate cotransporter Npt2a, which is primarily expressed in the proximal tubule, conferred kidney specificity to phosphate-stimulated G-3-P production. Importantly, exogenous G-3-P stimulated FGF23 production when Npt2a or Gpd1 were absent, confirming that it was the key circulating factor downstream of glycolytic phosphate sensing in the kidney. Together, these findings place glycolysis at the nexus of mineral and energy metabolism and identify a kidney-bone feedback loop that controls phosphate homeostasis.
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Affiliation(s)
- Wen Zhou
- Nephrology Division, Department of Medicine, and
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Petra Simic
- Nephrology Division, Department of Medicine, and
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Iris Y. Zhou
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Peter Caravan
- Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Xavier Vela Parada
- Nephrology Division, Department of Medicine, and
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Donghai Wen
- Nephrology Division, Department of Medicine, and
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Onica L. Washington
- Nephrology Division, Department of Medicine, and
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Maria Shvedova
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Kerry A. Pierce
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Clary B. Clish
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Michael Mannstadt
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Tatsuya Kobayashi
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Marc N. Wein
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Harald Jüppner
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
- Pediatric Nephrology Unit, Department of Pediatrics, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Eugene P. Rhee
- Nephrology Division, Department of Medicine, and
- Endocrine Unit, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA
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17
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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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18
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Andersen CG, Bavnhøj L, Pedersen BP. May the proton motive force be with you: A plant transporter review. Curr Opin Struct Biol 2023; 79:102535. [PMID: 36796226 DOI: 10.1016/j.sbi.2023.102535] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 11/28/2022] [Accepted: 01/03/2023] [Indexed: 02/16/2023]
Abstract
As our ecosystems experience challenges associated with climate change, an improved understanding of the fundamental biochemical processes governing plant physiology is needed. Strikingly, current structural information on plant membrane transporters is severely limited compared to other kingdoms of life, with only 18 unique structures in total. To advance future breakthroughs and insight in plant cell molecular biology, structural knowledge of membrane transporters is indispensable. This review summarizes the current status of structural knowledge in the plant membrane transporter field. Plants utilize the proton motive force (PMF) to drive secondary active transport. We discuss the PMF, how it relates to secondary active transport and provide a classification of PMF driven secondary active transport, discussing recently published structures of symporters, antiporters, and uniporters from plants.
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Affiliation(s)
| | - Laust Bavnhøj
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus C, Denmark. https://twitter.com/laustbavnhoej
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19
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Lehmann EF, Liziczai M, Drożdżyk K, Altermatt P, Langini C, Manolova V, Sundstrom H, Dürrenberger F, Dutzler R, Manatschal C. Structures of ferroportin in complex with its specific inhibitor vamifeport. eLife 2023; 12:e83053. [PMID: 36943194 PMCID: PMC10030120 DOI: 10.7554/elife.83053] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 02/27/2023] [Indexed: 03/18/2023] Open
Abstract
A central regulatory mechanism of iron homeostasis in humans involves ferroportin (FPN), the sole cellular iron exporter, and the peptide hormone hepcidin, which inhibits Fe2+ transport and induces internalization and degradation of FPN. Dysregulation of the FPN/hepcidin axis leads to diverse pathological conditions, and consequently, pharmacological compounds that inhibit FPN-mediated iron transport are of high clinical interest. Here, we describe the cryo-electron microscopy structures of human FPN in complex with synthetic nanobodies and vamifeport (VIT-2763), the first clinical-stage oral FPN inhibitor. Vamifeport competes with hepcidin for FPN binding and is currently in clinical development for β-thalassemia and sickle cell disease. The structures display two distinct conformations of FPN, representing outward-facing and occluded states of the transporter. The vamifeport site is located in the center of the protein, where the overlap with hepcidin interactions underlies the competitive relationship between the two molecules. The introduction of point mutations in the binding pocket of vamifeport reduces its affinity to FPN, emphasizing the relevance of the structural data. Together, our study reveals conformational rearrangements of FPN that are of potential relevance for transport, and it provides initial insight into the pharmacological targeting of this unique iron efflux transporter.
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Affiliation(s)
| | - Márton Liziczai
- Department of Biochemistry, University of ZurichZürichSwitzerland
| | | | | | - Cassiano Langini
- Department of Biochemistry, University of ZurichZürichSwitzerland
| | | | | | | | - Raimund Dutzler
- Department of Biochemistry, University of ZurichZürichSwitzerland
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20
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Arjun OK, Prakash T. Identification of conserved genomic signatures specific to Bifidobacterium species colonising the human gut. 3 Biotech 2023; 13:97. [PMID: 36852175 PMCID: PMC9958220 DOI: 10.1007/s13205-023-03492-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 01/25/2023] [Indexed: 02/26/2023] Open
Abstract
Bifidobacterium species are known for their ability to inhabit various habitats and are often regarded as the first colonisers of the human gut. In the present work, we have used comparative genomics to identify conserved genomic signatures specific to Bifidobacterium species associated with the human gut. Our approach discovered five genomic signatures with varying lengths and confidence. Among the predicted five signatures, a 1790 bp multi-drug resistance (MDR) signature was found to be remarkably specific to only those species that can colonise the human gut. The signature codes for a membrane transport protein belonging to the major facilitator superfamily (MFS) generally involved in MDR. Phylogenetic analyses of the MDR signature suggest a lineage-specific evolution of the MDR signature in bifidobacteria colonising the human gut. Functional annotation led to the discovery of two conserved domains in the protein; a catalytic MFS domain involved in the efflux of drugs and toxins, and a regulatory cystathionine-β-synthase (CBS) domain that can interact with adenosyl-carriers. Molecular docking simulation performed with the modelled tertiary structure of the MDR signature revealed the putative functional role of the covalently linked domains. The MFS domain displayed a high affinity towards various protein synthesis inhibitor antibiotics and human bile acids, whereas the C-terminally linked CBS domain exhibited favourable binding with molecular structures of ATP and AMP. Therefore, we believe that the predicted signature represents a niche-specific survival trait involved in bile and antibiotic resistance, imparting an adaptive advantage to the Bifidobacterium species colonising the human gut. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03492-4.
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Affiliation(s)
- O. K. Arjun
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005 India
| | - Tulika Prakash
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, Himachal Pradesh 175005 India
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21
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Blaimschein N, Hariharan P, Manioglu S, Guan L, Müller DJ. Substrate-binding guides individual melibiose permeases MelB to structurally soften and to destabilize cytoplasmic middle-loop C3. Structure 2023; 31:58-67.e4. [PMID: 36525976 PMCID: PMC9825662 DOI: 10.1016/j.str.2022.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/06/2022] [Accepted: 11/18/2022] [Indexed: 12/23/2022]
Abstract
The melibiose permease MelB is a well-studied Na+-coupled transporter of the major facilitator superfamily. However, the symport mechanism of galactosides and cations is still not fully understood, especially at structural levels. Here, we use single-molecule force spectroscopy to investigate substrate-induced structural changes of MelB from Salmonella typhimurium. In the absence of substrate, MelB equally populates two different states, from which one shows higher mechanical structural stability with additional stabilization of the cytoplasmic middle-loop C3. In the presence of either melibiose or a coupling Na+-cation, however, MelB increasingly populates the mechanically less stable state, which shows a destabilized middle-loop C3. In the presence of both substrate and co-substrate, this mechanically less stable state of MelB is predominant. Our findings describe how both substrates guide MelB transporters to populate two different mechanically stabilized states, and contribute mechanistic insights to the alternating-access action for the galactoside/cation symport catalyzed by MelB.
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Affiliation(s)
- Nina Blaimschein
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Selen Manioglu
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA.
| | - Daniel J Müller
- Department of Biosystems Science and Engineering, Eidgenössische Technische Hochschule (ETH) Zürich, 4058 Basel, Switzerland.
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22
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Dang Y, Zhou D, Du X, Zhao H, Lee CH, Yang J, Wang Y, Qin C, Guo Z, Zhang Z. Molecular mechanism of substrate recognition by folate transporter SLC19A1. Cell Discov 2022; 8:141. [PMID: 36575193 PMCID: PMC9794768 DOI: 10.1038/s41421-022-00508-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/09/2022] [Indexed: 12/29/2022] Open
Abstract
Folate (vitamin B9) is the coenzyme involved in one-carbon transfer biochemical reactions essential for cell survival and proliferation, with its inadequacy causing developmental defects or severe diseases. Notably, mammalian cells lack the ability to de novo synthesize folate but instead rely on its intake from extracellular sources via specific transporters or receptors, among which SLC19A1 is the ubiquitously expressed one in tissues. However, the mechanism of substrate recognition by SLC19A1 remains unclear. Here we report the cryo-EM structures of human SLC19A1 and its complex with 5-methyltetrahydrofolate at 3.5-3.6 Å resolution and elucidate the critical residues for substrate recognition. In particular, we reveal that two variant residues among SLC19 subfamily members designate the specificity for folate. Moreover, we identify intracellular thiamine pyrophosphate as the favorite coupled substrate for folate transport by SLC19A1. Together, this work establishes the molecular basis of substrate recognition by this central folate transporter.
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Affiliation(s)
- Yu Dang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Dong Zhou
- grid.11135.370000 0001 2256 9319Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Xiaojuan Du
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China ,grid.411472.50000 0004 1764 1621Present Address: Peking University First Hospital, Peking University Health Science Center, Beijing, China
| | - Hongtu Zhao
- grid.240871.80000 0001 0224 711XDepartment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Chia-Hsueh Lee
- grid.240871.80000 0001 0224 711XDepartment of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN USA
| | - Jing Yang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China
| | - Yijie Wang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China
| | - Changdong Qin
- grid.11135.370000 0001 2256 9319Cryo-EM Platform, School of Life Sciences, Peking University, Beijing, China
| | - Zhenxi Guo
- grid.11135.370000 0001 2256 9319Cryo-EM Platform, School of Life Sciences, Peking University, Beijing, China
| | - Zhe Zhang
- grid.11135.370000 0001 2256 9319State Key Laboratory of Membrane Biology, Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China ,grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, Beijing, China
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23
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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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24
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Dastvan R, Rasouli A, Dehghani-Ghahnaviyeh S, Gies S, Tajkhorshid E. Proton-driven alternating access in a spinster lipid transporter. Nat Commun 2022; 13:5161. [PMID: 36055994 PMCID: PMC9440201 DOI: 10.1038/s41467-022-32759-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/16/2022] [Indexed: 11/16/2022] Open
Abstract
Spinster (Spns) lipid transporters are critical for transporting sphingosine-1-phosphate (S1P) across cellular membranes. In humans, Spns2 functions as the main S1P transporter in endothelial cells, making it a potential drug target for modulating S1P signaling. Here, we employed an integrated approach in lipid membranes to identify unknown conformational states of a bacterial Spns from Hyphomonas neptunium (HnSpns) and to define its proton- and substrate-coupled conformational dynamics. Our systematic study reveals conserved residues critical for protonation steps and their regulation, and how sequential protonation of these proton switches coordinates the conformational transitions in the context of a noncanonical ligand-dependent alternating access. A conserved periplasmic salt bridge (Asp60TM2:Arg289TM7) keeps the transporter in a closed conformation, while proton-dependent conformational dynamics are significantly enhanced on the periplasmic side, providing a pathway for ligand exchange.
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Affiliation(s)
- Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA.
| | - Ali Rasouli
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sepehr Dehghani-Ghahnaviyeh
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Samantha Gies
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO, 63104, USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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25
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Asin-Garcia E, Batianis C, Li Y, Fawcett JD, de Jong I, Dos Santos VAPM. Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida. Microb Cell Fact 2022; 21:156. [PMID: 35934698 PMCID: PMC9358898 DOI: 10.1186/s12934-022-01883-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 07/26/2022] [Indexed: 11/12/2022] Open
Abstract
The inclusion of biosafety strategies into strain engineering pipelines is crucial for safe-by-design biobased processes. This in turn might enable a more rapid regulatory acceptance of bioengineered organisms in both industrial and environmental applications. For this reason, we equipped the industrially relevant microbial chassis Pseudomonas putida KT2440 with an effective biocontainment strategy based on a synthetic dependency on phosphite, which is generally not readily available in the environment. The produced PSAG-9 strain was first engineered to assimilate phosphite through the genome-integration of a phosphite dehydrogenase and a phosphite-specific transport complex. Subsequently, to deter the strain from growing on naturally assimilated phosphate, all native genes related to its transport were identified and deleted generating a strain unable to grow on media containing any phosphorous source other than phosphite. PSAG-9 exhibited fitness levels with phosphite similar to those of the wild type with phosphate, and low levels of escape frequency. Beyond biosafety, this strategy endowed P. putida with the capacity to be cultured under non-sterile conditions using phosphite as the sole phosphorous source with a reduced risk of contamination by other microbes, while displaying enhanced NADH regenerative capacity. These industrially beneficial features complement the metabolic advantages for which this species is known for, thereby strengthening it as a synthetic biology chassis with potential uses in industry, with suitability towards environmental release.
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Affiliation(s)
- Enrique Asin-Garcia
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Christos Batianis
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - Yunsong Li
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
| | - James D Fawcett
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, SW72BX, UK
| | - Ivar de Jong
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, 6708 WE, The Netherlands.
- LifeGlimmer GmbH, 12163, Berlin, Germany.
- Bioprocess Engineering Group, Wageningen University & Research, Wageningen, 6700 AA, The Netherlands.
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26
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Effect of New 2-Thioxoimidazolidin-4-one Compounds against Staphylococcus aureus Clinical Strains and Immunological Markers’ Combinations. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:6720241. [PMID: 35873361 PMCID: PMC9300335 DOI: 10.1155/2022/6720241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 04/03/2022] [Accepted: 04/07/2022] [Indexed: 12/03/2022]
Abstract
Although the structure-activity relationship indicates that the 4-thioxoimidazolidin ring is essential for antibacterial activities and pharmaceutical applications, there were no enough studies on the derivatives of this compound. Evaluating the new hydantoin compounds C5 (3-((2-bromobenzylidene) amino)-2- thioxoimidazolidin-4-one) and C6 (3-((4- methoxybenzylidene) amino)-2-thioxoimidazolidin-4-one) that were prepared against clinical Staphylococcus aureus isolates for antibacterial, antibiofilm, and antihemagglutination activities is the aim of this study. Therefore, the potential clinical resistance of the strains was evaluated by their ability to form biofilms, antibiotic resistance, and agglutinate erythrocytes macroscopically and microscopically; besides, the bacterial biofilm was screened for any association with the patient's serum immunoglobulin levels and complements. Despite the effective concentration for C5 and C6 compounds, which is ≤ 31.25 μg/ml, the reduction rate is not concentration-dependent; it depends on the molecular docking of the hydantoin compounds. Hence, the effect of the minimal inhibitory concentrations (MICs) is variable. In this study, the results for the compounds (with the concentration of 31.25–62.5 μg/mL for C5 and 62.5–125 μg/mL for C6) significantly manifest the antibacteria, antibiofilm, and antihemagglutination effects against the virulent strains of S. aureus due to the high percentage of biofilm inhibition that was caused by the new hydantoin compounds. Besides, time-kill kinetics studies showed that these compounds pose bactericidal action. Overall, this study revealed that the new hydantoin derivatives have an interesting potential as new antibacterial drugs through the inhibition of bacterial adhesion. The infections of these isolates activate the complement system through the lectin pathway. Nevertheless, these compounds can be improved in order to be used at even lower concentrations.
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27
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Chavarria-Pizarro T, Resl P, Kuhl-Nagel T, Janjic A, Fernandez Mendoza F, Werth S. Antibiotic-Induced Treatments Reveal Stress-Responsive Gene Expression in the Endangered Lichen Lobaria pulmonaria. J Fungi (Basel) 2022; 8:jof8060625. [PMID: 35736108 PMCID: PMC9225190 DOI: 10.3390/jof8060625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022] Open
Abstract
Antibiotics are primarily found in the environment due to human activity, which has been reported to influence the structure of biotic communities and the ecological functions of soil and water ecosystems. Nonetheless, their effects in other terrestrial ecosystems have not been well studied. As a result of oxidative stress in organisms exposed to high levels of antibiotics, genotoxicity can lead to DNA damage and, potentially, cell death. In addition, in symbiotic organisms, removal of the associated microbiome by antibiotic treatment has been observed to have a big impact on the host, e.g., corals. The lung lichen Lobaria pulmonaria has more than 800 associated bacterial species, a microbiome which has been hypothesized to increase the lichen's fitness. We artificially exposed samples of L. pulmonaria to antibiotics and a stepwise temperature increase to determine the relative effects of antibiotic treatments vs. temperature on the mycobiont and photobiont gene expression and the viability and on the community structure of the lichen-associated bacteria. We found that the mycobiont and photobiont highly reacted to different antibiotics, independently of temperature exposure. We did not find major differences in bacterial community composition or alpha diversity between antibiotic treatments and controls. For these reasons, the upregulation of stress-related genes in antibiotic-treated samples could be caused by genotoxicity in L. pulmonaria and its photobiont caused by exposure to antibiotics, and the observed stress responses are reactions of the symbiotic partners to reduce damage to their cells. Our study is of great interest for the community of researchers studying symbiotic organisms as it represents one of the first steps to understanding gene expression in an endangered lichen in response to exposure to toxic environments, along with dynamics in its associated bacterial communities.
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Affiliation(s)
- Tania Chavarria-Pizarro
- Systematics, Biodiversity and Evolution of Plants, Faculty of Biology, LMU Munich, Menzingerstraße 67, 80638 Munich, Germany;
- Correspondence: (T.C.-P.); (S.W.)
| | - Philipp Resl
- Systematics, Biodiversity and Evolution of Plants, Faculty of Biology, LMU Munich, Menzingerstraße 67, 80638 Munich, Germany;
- Institute of Biology, University of Graz, Universitätsplatz 2, 8010 Graz, Austria;
| | - Theresa Kuhl-Nagel
- Helmholtz Center Munich, German Research Center for Environmental Health, Institute for Network Biology (INET), Ingolstädter Landstraße 1, 85764 Neuherberg, Germany;
| | - Aleksandar Janjic
- Anthropology and Human Genomics, Faculty of Biology, LMU Munich, Großhaderner Straße 2-4, 82152 Planegg-Martinsried, Germany;
| | | | - Silke Werth
- Systematics, Biodiversity and Evolution of Plants, Faculty of Biology, LMU Munich, Menzingerstraße 67, 80638 Munich, Germany;
- Correspondence: (T.C.-P.); (S.W.)
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28
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Proton Coupling and the Multiscale Kinetic Mechanism of a Peptide Transporter. Biophys J 2022; 121:2266-2278. [PMID: 35614850 DOI: 10.1016/j.bpj.2022.05.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/13/2022] [Accepted: 05/19/2022] [Indexed: 11/02/2022] Open
Abstract
Proton coupled peptide transporters (POTs) are crucial for the uptake of di- and tri-peptides as well as drug and pro-drug molecules in prokaryotes and eukaryotic cells. We illustrate from multiscale modeling how transmembrane proton flux couples within a POT protein to drive essential steps of the full functional cycle: 1) protonation of a glutamate on transmembrane helix (TM) 7 opens the extracellular gate, allowing ligand entry; 2) inward proton flow induces the cytosolic release of ligand by varying the protonation state of a second conserved glutamate on TM10; 3) proton movement between TM7 and TM10 is thermodynamically driven and kinetically permissible via water proton shuttling without the participation of ligand. Our results, for the first time, give direct computational confirmation for the alternating access model of POTs, and point to a quantitative multiscale kinetic picture of the functioning protein mechanism.
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29
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Sharma S, Banerjee A, Moreno A, Redhu AK, Falson P, Prasad R. Spontaneous Suppressors against Debilitating Transmembrane Mutants of CaMdr1 Disclose Novel Interdomain Communication via Signature Motifs of the Major Facilitator Superfamily. J Fungi (Basel) 2022; 8:538. [PMID: 35628792 PMCID: PMC9143388 DOI: 10.3390/jof8050538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 05/13/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
The Major Facilitator Superfamily (MFS) drug:H+ antiporter CaMdr1, from Candida albicans, is responsible for the efflux of structurally diverse antifungals. MFS members share a common fold of 12−14 transmembrane helices (TMHs) forming two N- and C-domains. Each domain is arranged in a pseudo-symmetric fold of two tandems of 3-TMHs that alternatively expose the drug-binding site towards the inside or the outside of the yeast to promote drug binding and release. MFS proteins show great diversity in primary structure and few conserved signature motifs, each thought to have a common function in the superfamily, although not yet clearly established. Here, we provide new information on these motifs by having screened a library of 64 drug transport-deficient mutants and their corresponding suppressors spontaneously addressing the deficiency. We found that five strains recovered the drug-resistance capacity by expressing CaMdr1 with a secondary mutation. The pairs of debilitating/rescuing residues are distributed either in the same TMH (T127ATMH1- > G140DTMH1) or 3-TMHs repeat (F216ATMH4- > G260ATMH5), at the hinge of 3-TMHs repeats tandems (R184ATMH3- > D235HTMH4, L480ATMH10- > A435TTMH9), and finally between the N- and C-domains (G230ATMH4- > P528HTMH12). Remarkably, most of these mutants belong to the different signature motifs, highlighting a mechanistic role and interplay thought to be conserved among MFS proteins. Results also point to the specific role of TMH11 in the interplay between the N- and C-domains in the inward- to outward-open conformational transition.
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Affiliation(s)
- Suman Sharma
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India; (S.S.); (A.B.)
| | - Atanu Banerjee
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India; (S.S.); (A.B.)
| | - Alexis Moreno
- Drug Resistance & Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry Laboratory, Institut de Biologie et Chimie des Protéines, CNRS-Lyon 1 University Research lab n° 5086, 69367 Lyon, France;
| | | | - Pierre Falson
- Drug Resistance & Membrane Proteins Team, Molecular Microbiology and Structural Biochemistry Laboratory, Institut de Biologie et Chimie des Protéines, CNRS-Lyon 1 University Research lab n° 5086, 69367 Lyon, France;
| | - Rajendra Prasad
- Amity Institute of Biotechnology, Amity University Haryana, Gurugram 122413, India; (S.S.); (A.B.)
- Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram 122413, India
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30
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Sauer DB, Marden JJ, Sudar JC, Song J, Mulligan C, Wang DN. Structural basis of ion - substrate coupling in the Na +-dependent dicarboxylate transporter VcINDY. Nat Commun 2022; 13:2644. [PMID: 35551191 PMCID: PMC9098524 DOI: 10.1038/s41467-022-30406-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/28/2022] [Indexed: 11/21/2022] Open
Abstract
The Na+-dependent dicarboxylate transporter from Vibrio cholerae (VcINDY) is a prototype for the divalent anion sodium symporter (DASS) family. While the utilization of an electrochemical Na+ gradient to power substrate transport is well established for VcINDY, the structural basis of this coupling between sodium and substrate binding is not currently understood. Here, using a combination of cryo-EM structure determination, succinate binding and site-directed cysteine alkylation assays, we demonstrate that the VcINDY protein couples sodium- and substrate-binding via a previously unseen cooperative mechanism by conformational selection. In the absence of sodium, substrate binding is abolished, with the succinate binding regions exhibiting increased flexibility, including HPinb, TM10b and the substrate clamshell motifs. Upon sodium binding, these regions become structurally ordered and create a proper binding site for the substrate. Taken together, these results provide strong evidence that VcINDY's conformational selection mechanism is a result of the sodium-dependent formation of the substrate binding site.
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Affiliation(s)
- David B Sauer
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
- Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Jennifer J Marden
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Joseph C Sudar
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | - Jinmei Song
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA
| | | | - Da-Neng Wang
- Department of Cell Biology, New York University School of Medicine, New York, NY, 10016, USA.
- Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, NY, 10016, USA.
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Insights into the structure and function of the human organic anion transporter 1 in lipid bilayer membranes. Sci Rep 2022; 12:7057. [PMID: 35488116 PMCID: PMC9054760 DOI: 10.1038/s41598-022-10755-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/12/2022] [Indexed: 01/27/2023] Open
Abstract
The human SLC22A6/OAT1 plays an important role in the elimination of a broad range of endogenous substances and xenobiotics thus attracting attention from the pharmacological community. Furthermore, OAT1 is also involved in key physiological events such as the remote inter-organ communication. Despite its significance, the knowledge about hOAT1 structure and the transport mechanism at the atomic level remains fragmented owing to the lack of resolved structures. By means of protein-threading modeling refined by μs-scaled Molecular Dynamics simulations, the present study provides the first robust model of hOAT1 in outward-facing conformation. Taking advantage of the AlphaFold 2 predicted structure of hOAT1 in inward-facing conformation, we here provide the essential structural and functional features comparing both states. The intracellular motifs conserved among Major Facilitator Superfamily members create a so-called “charge-relay system” that works as molecular switches modulating the conformation. The principal element of the event points at interactions of charged residues that appear crucial for the transporter dynamics and function. Moreover, hOAT1 model was embedded in different lipid bilayer membranes highlighting the crucial structural dependence on lipid-protein interactions. MD simulations supported the pivotal role of phosphatidylethanolamine components to the protein conformation stability. The present model is made available to decipher the impact of any observed polymorphism and mutation on drug transport as well as to understand substrate binding modes.
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Xie X, Lai W, Che X, Wang S, Ren Y, Hu W, Chen H, Tang M. A SPX domain-containing phosphate transporter from Rhizophagus irregularis handles phosphate homeostasis at symbiotic interface of arbuscular mycorrhizas. THE NEW PHYTOLOGIST 2022; 234:650-671. [PMID: 35037255 DOI: 10.1111/nph.17973] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 12/22/2021] [Indexed: 05/28/2023]
Abstract
Reciprocal symbiosis of > 70% of terrestrial vascular plants with arbuscular mycorrhizal (AM) fungi provides the fungi with fatty acids and sugars. In return, AM fungi facilitate plant phosphate (Pi) uptake from soil. However, how AM fungi handle Pi transport and homeostasis at the symbiotic interface of AM symbiosis is poorly understood. Here, we identify an SPX (SYG1/Pho81/XPR1) domain-containing phosphate transporter, RiPT7 from Rhizophagus irregularis. To characterize the RiPT7 transporter, we combined subcellular localization and heterologous expression studies in yeasts with reverse genetics approaches during the in planta phase. The results show that RiPT7 is conserved across fungal species and expressed in the intraradical mycelia. It is expressed in the arbuscules, intraradical hyphae and vesicles, independently of Pi availability. The plasma membrane-localized RiPT7 facilitates bidirectional Pi transport, depending on Pi gradient across the plasma membrane, whereas the SPX domain of RiPT7 inhibits Pi transport activity and mediates the vacuolar targeting of RiPT7 in yeast in response to Pi starvation. Importantly, RiPT7 silencing hampers arbuscule development of R. irregularis and symbiotic Pi delivery under medium- to low-Pi conditions. Collectively, our findings reveal a role for RiPT7 in fine-tuning of Pi homeostasis across the fungal membrane to maintain the AM development.
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Affiliation(s)
- Xianan Xie
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Wenzhen Lai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Xianrong Che
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Sijia Wang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ying Ren
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Wentao Hu
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Hui Chen
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ming Tang
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
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Structural basis for inhibition of the drug efflux pump NorA from Staphylococcus aureus. Nat Chem Biol 2022; 18:706-712. [PMID: 35361990 PMCID: PMC9246859 DOI: 10.1038/s41589-022-00994-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 02/08/2022] [Indexed: 11/08/2022]
Abstract
Membrane protein efflux pumps confer antibiotic resistance by extruding structurally distinct compounds and lowering their intracellular concentration. Yet, there are no clinically approved drugs to inhibit efflux pumps, which would potentiate the efficacy of existing antibiotics rendered ineffective by drug efflux. Here we identified synthetic antigen-binding fragments (Fabs) that inhibit the quinolone transporter NorA from methicillin-resistant Staphylococcus aureus (MRSA). Structures of two NorA-Fab complexes determined using cryo-electron microscopy reveal a Fab loop deeply inserted in the substrate-binding pocket of NorA. An arginine residue on this loop interacts with two neighboring aspartate and glutamate residues essential for NorA-mediated antibiotic resistance in MRSA. Peptide mimics of the Fab loop inhibit NorA with submicromolar potency and ablate MRSA growth in combination with the antibiotic norfloxacin. These findings establish a class of peptide inhibitors that block antibiotic efflux in MRSA by targeting indispensable residues in NorA without the need for membrane permeability.
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Beckstein O, Naughton F. General principles of secondary active transporter function. BIOPHYSICS REVIEWS 2022; 3:011307. [PMID: 35434715 PMCID: PMC8984959 DOI: 10.1063/5.0047967] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Accepted: 02/23/2022] [Indexed: 04/13/2023]
Abstract
Transport of ions and small molecules across the cell membrane against electrochemical gradients is catalyzed by integral membrane proteins that use a source of free energy to drive the energetically uphill flux of the transported substrate. Secondary active transporters couple the spontaneous influx of a "driving" ion such as Na+ or H+ to the flux of the substrate. The thermodynamics of such cyclical non-equilibrium systems are well understood, and recent work has focused on the molecular mechanism of secondary active transport. The fact that these transporters change their conformation between an inward-facing and outward-facing conformation in a cyclical fashion, called the alternating access model, is broadly recognized as the molecular framework in which to describe transporter function. However, only with the advent of high resolution crystal structures and detailed computer simulations, it has become possible to recognize common molecular-level principles between disparate transporter families. Inverted repeat symmetry in secondary active transporters has shed light onto how protein structures can encode a bi-stable two-state system. Based on structural data, three broad classes of alternating access transitions have been described as rocker-switch, rocking-bundle, and elevator mechanisms. More detailed analysis indicates that transporters can be understood as gated pores with at least two coupled gates. These gates are not just a convenient cartoon element to illustrate a putative mechanism but map to distinct parts of the transporter protein. Enumerating all distinct gate states naturally includes occluded states in the alternating access picture and also suggests what kind of protein conformations might be observable. By connecting the possible conformational states and ion/substrate bound states in a kinetic model, a unified picture emerges in which the symporter, antiporter, and uniporter functions are extremes in a continuum of functionality. As usual with biological systems, few principles and rules are absolute and exceptions are discussed as well as how biological complexity may be integrated in quantitative kinetic models that may provide a bridge from the structure to function.
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Affiliation(s)
- Oliver Beckstein
- Department of Physics, Arizona State University, Tempe, Arizona 85287, USA
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35
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Stauffer M, Jeckelmann JM, Ilgü H, Ucurum Z, Boggavarapu R, Fotiadis D. Peptide transporter structure reveals binding and action mechanism of a potent PEPT1 and PEPT2 inhibitor. Commun Chem 2022; 5:23. [PMID: 36697632 PMCID: PMC9814568 DOI: 10.1038/s42004-022-00636-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/27/2022] [Indexed: 01/28/2023] Open
Abstract
Inhibitors for membrane transporters have been shown to be indispensable as drugs and tool compounds. The proton-dependent oligopeptide transporters PEPT1 and PEPT2 from the SLC15 family play important roles in human and mammalian physiology. With Lys[Z(NO2)]-Val (LZNV), a modified Lys-Val dipeptide, a potent transport inhibitor for PEPT1 and PEPT2 is available. Here we present the crystal structure of the peptide transporter YePEPT in complex with LZNV. The structure revealed the molecular interactions for inhibitor binding and a previously undescribed mostly hydrophobic pocket, the PZ pocket, involved in interaction with LZNV. Comparison with a here determined ligand-free structure of the transporter unveiled that the initially absent PZ pocket emerges through conformational changes upon inhibitor binding. The provided biochemical and structural information constitutes an important framework for the mechanistic understanding of inhibitor binding and action in proton-dependent oligopeptide transporters.
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Affiliation(s)
- Mirko Stauffer
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Jean-Marc Jeckelmann
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Hüseyin Ilgü
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Zöhre Ucurum
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
| | - Rajendra Boggavarapu
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland ,grid.67105.350000 0001 2164 3847Present Address: Department of Physiology and Biophysics, Case Western Reserve University, Cleveland, OH USA
| | - Dimitrios Fotiadis
- grid.5734.50000 0001 0726 5157Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, Bern, Switzerland
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Lambert E, Mehdipour AR, Schmidt A, Hummer G, Perez C. Evidence for a trap-and-flip mechanism in a proton-dependent lipid transporter. Nat Commun 2022; 13:1022. [PMID: 35197476 PMCID: PMC8866510 DOI: 10.1038/s41467-022-28361-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 01/23/2022] [Indexed: 02/08/2023] Open
Abstract
Transport of lipids across membranes is fundamental for diverse biological pathways in cells. Multiple ion-coupled transporters take part in lipid translocation, but their mechanisms remain largely unknown. Major facilitator superfamily (MFS) lipid transporters play central roles in cell wall synthesis, brain development and function, lipids recycling, and cell signaling. Recent structures of MFS lipid transporters revealed overlapping architectural features pointing towards a common mechanism. Here we used cysteine disulfide trapping, molecular dynamics simulations, mutagenesis analysis, and transport assays in vitro and in vivo, to investigate the mechanism of LtaA, a proton-dependent MFS lipid transporter essential for lipoteichoic acid synthesis in the pathogen Staphylococcus aureus. We reveal that LtaA displays asymmetric lateral openings with distinct functional relevance and that cycling through outward- and inward-facing conformations is essential for transport activity. We demonstrate that while the entire amphipathic central cavity of LtaA contributes to lipid binding, its hydrophilic pocket dictates substrate specificity. We propose that LtaA catalyzes lipid translocation by a ‘trap-and-flip’ mechanism that might be shared among MFS lipid transporters. LtaA catalyzes glycolipid translocation by a ‘trap-and-flip’ mechanism, pointing to a shared mechanistic model among MFS lipid transporters. Asymmetric lateral openings allow access of the entire lipid substrate to the amphipathic central cavity.
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Affiliation(s)
| | | | - Alexander Schmidt
- Proteomics Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gerhard Hummer
- Institute of Biophysics, Goethe University Frankfurt, Frankfurt am Main, Germany.,Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Camilo Perez
- Biozentrum, University of Basel, Basel, Switzerland.
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Sadessa K, Beyene Y, Ifie BE, Suresh LM, Olsen MS, Ogugo V, Wegary D, Tongoona P, Danquah E, Offei SK, Prasanna BM, Gowda M. Identification of Genomic Regions Associated with Agronomic and Disease Resistance Traits in a Large Set of Multiple DH Populations. Genes (Basel) 2022; 13:genes13020351. [PMID: 35205395 PMCID: PMC8872035 DOI: 10.3390/genes13020351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/17/2022] Open
Abstract
Breeding maize lines with the improved level of desired agronomic traits under optimum and drought conditions as well as increased levels of resistance to several diseases such as maize lethal necrosis (MLN) is one of the most sustainable approaches for the sub-Saharan African region. In this study, 879 doubled haploid (DH) lines derived from 26 biparental populations were evaluated under artificial inoculation of MLN, as well as under well-watered (WW) and water-stressed (WS) conditions for grain yield and other agronomic traits. All DH lines were used for analyses of genotypic variability, association studies, and genomic predictions for the grain yield and other yield-related traits. Genome-wide association study (GWAS) using a mixed linear FarmCPU model identified SNPs associated with the studied traits i.e., about seven and eight SNPs for the grain yield; 16 and 12 for anthesis date; seven and eight for anthesis silking interval; 14 and 5 for both ear and plant height; and 15 and 5 for moisture under both WW and WS environments, respectively. Similarly, about 13 and 11 SNPs associated with gray leaf spot and turcicum leaf blight were identified. Eleven SNPs associated with senescence under WS management that had depicted drought-stress-tolerant QTLs were identified. Under MLN artificial inoculation, a total of 12 and 10 SNPs associated with MLN disease severity and AUDPC traits, respectively, were identified. Genomic prediction under WW, WS, and MLN disease artificial inoculation revealed moderate-to-high prediction accuracy. The findings of this study provide useful information on understanding the genetic basis for the MLN resistance, grain yield, and other agronomic traits under MLN artificial inoculation, WW, and WS conditions. Therefore, the obtained information can be used for further validation and developing functional molecular markers for marker-assisted selection and for implementing genomic prediction to develop superior elite lines.
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Affiliation(s)
- Kassahun Sadessa
- Ethiopian Institute of Agricultural Research (EIAR), Ambo Agricultural Research Center, Ambo P.O. Box 37, West Shoa, Ethiopia;
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
- International Maize and Wheat Improvement Center (CIMMYT), 12.5 KM Peg, Harare P.O. Box MP163, Zimbabwe;
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Beatrice E. Ifie
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - L. M. Suresh
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Michael S. Olsen
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Veronica Ogugo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Dagne Wegary
- International Maize and Wheat Improvement Center (CIMMYT), 12.5 KM Peg, Harare P.O. Box MP163, Zimbabwe;
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Eric Danquah
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, P.O. Box LG23, Accra 00233, Ghana; (B.E.I.); (P.T.); (E.D.); (S.K.O.)
| | - Boddupalli M. Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, P.O. Box 1041-00621, Nairobi 00100, Kenya; (Y.B.); (L.M.S.); (M.S.O.); (V.O.); (B.M.P.)
- Correspondence: ; Tel.: +254-727019454
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Cao GH, Wang XF, Li ZD, Zhang X, Li XG, Gu W, Zhang F, Yu J, He S. A Panax notoginseng phosphate transporter, PnPht1;3, greatly contributes to phosphate and arsenate uptake. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:259-271. [PMID: 35115080 DOI: 10.1071/fp21218] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 12/17/2021] [Indexed: 06/14/2023]
Abstract
The crisis of arsenic (As) accumulation in rhizomes threatens the quality and safety of Panax notoginseng (Burk.) F.H. Chen, which is a well-known traditional Chinese herb with a long clinical history. The uptake of arsenate (AsV) could be suppressed by supplying phosphate (Pi), in which Pi transporters play important roles in the uptake of Pi and AsV. Herein, the P . notoginseng Pi transporter-encoding gene PnPht1;3 was identified and characterised under Pi deficiency and AsV exposure. In this study, the open reading frame (ORF) of PnPht1;3 was cloned according to RNA-seq and encoded 545 amino acids. The relative expression levels revealed that PnPht1;3 was significantly upregulated under phosphate deficiency and AsV exposure. Heterologous expression in Saccharomyces cerevisiae MB192 demonstrated that PnPht1;3 performed optimally in complementing the yeast Pi-transport defect and accumulated more As in the cells. Combined with the subcellular localisation prediction, it was concluded that PnPht1;3 encodes a functional plasma membrane-localised transporter protein that mediates putative high-affinity Pi/H+ symport activity and enhances the uptake of Pi and AsV. Therefore, a better understanding of the roles of the P . notoginseng Pi transporter could provide new insight for solving As accumulation in medicinal plants.
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Affiliation(s)
- Guan-Hua Cao
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Xi-Fu Wang
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Ze-Dong Li
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Xue Zhang
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Xiao-Gang Li
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Wen Gu
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Fan Zhang
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Jie Yu
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
| | - Sen He
- School of Chinese Materia Medica and Yunnan Key Laboratory of Southern Medicine Utilization, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China; and Yunnan Key Laboratory for Dai and Yi Medicines, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, China
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Gupta S, Kumar C, Shrivastava K, Chauhan V, Singh A, Arora R, Giri A, Cabibbe AM, Sharma NK, Spitaleri A, Cirillo DM, Bose M, Varma-Basil M. Whole genome sequencing of isoniazid monoresistant clinical isolates of Mycobacterium tuberculosis reveals novel genetic polymorphisms. Tuberculosis (Edinb) 2022; 133:102173. [DOI: 10.1016/j.tube.2022.102173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/29/2021] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
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40
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Park Y, Solhtalab M, Thongsomboon W, Aristilde L. Strategies of organic phosphorus recycling by soil bacteria: acquisition, metabolism, and regulation. ENVIRONMENTAL MICROBIOLOGY REPORTS 2022; 14:3-24. [PMID: 35001516 PMCID: PMC9306846 DOI: 10.1111/1758-2229.13040] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 12/07/2021] [Accepted: 12/14/2021] [Indexed: 05/12/2023]
Abstract
Critical to meeting cellular phosphorus (P) demand, soil bacteria deploy a number of strategies to overcome limitation in inorganic P (Pi ) in soils. As a significant contributor to P recycling, soil bacteria secrete extracellular enzymes to degrade organic P (Po ) in soils into the readily bioavailable Pi . In addition, several Po compounds can be transported directly via specific transporters and subsequently enter intracellular metabolic pathways. In this review, we highlight the strategies that soil bacteria employ to recycle Po from the soil environment. We discuss the diversity of extracellular phosphatases in soils, the selectivity of these enzymes towards various Po biomolecules and the influence of the soil environmental conditions on the enzyme's activities. Moreover, we outline the intracellular metabolic pathways for Po biosynthesis and transporter-assisted Po and Pi uptake at different Pi availabilities. We further highlight the regulatory mechanisms that govern the production of phosphatases, the expression of Po transporters and the key metabolic changes in P metabolism in response to environmental Pi availability. Due to the depletion of natural resources for Pi , we propose future studies needed to leverage bacteria-mediated P recycling from the large pools of Po in soils or organic wastes to benefit agricultural productivity.
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Affiliation(s)
- Yeonsoo Park
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Mina Solhtalab
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
| | - Wiriya Thongsomboon
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Chemistry, Faculty of ScienceMahasarakham UniversityMahasarakham44150Thailand
| | - Ludmilla Aristilde
- Department of Civil and Environmental Engineering, McCormick School of Engineering and Applied ScienceNorthwestern UniversityEvanstonIL60208USA
- Department of Biological and Environmental EngineeringCornell University, Riley‐Robb HallIthacaNY14853USA
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High-speed atomic force microscopy reveals a three-state elevator mechanism in the citrate transporter CitS. Proc Natl Acad Sci U S A 2022; 119:2113927119. [PMID: 35101979 PMCID: PMC8833178 DOI: 10.1073/pnas.2113927119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2021] [Indexed: 12/16/2022] Open
Abstract
As cellular membranes are impermeable to most molecules, transporter proteins are typically present in the membrane to transport small molecules in or out of the cell. Due to the small, nanometer size of these transporters, it is challenging to study their transport mechanism. Here, we use advanced microscopy approaches to study in real time and at the single-molecule level the mode of action of the dimeric CitS tranpsorter. Using high-speed atomic force microscopy, we visualize the dynamic, elevator-like movement of the transporter, and we reveal that the two protomers move independently. We also discovered an intermediate state, reminiscent of another, unrelated transporter, indicating that independent evolutionary pathways have led to similar three-state elevator mechanisms. The secondary active transporter CitS shuttles citrate across the cytoplasmic membrane of gram-negative bacteria by coupling substrate translocation to the transport of two Na+ ions. Static crystal structures suggest an elevator type of transport mechanism with two states: up and down. However, no dynamic measurements have been performed to substantiate this assumption. Here, we use high-speed atomic force microscopy for real-time visualization of the transport cycle at the level of single transporters. Unexpectedly, instead of a bimodal height distribution for the up and down states, the experiments reveal movements between three distinguishable states, with protrusions of ∼0.5 nm, ∼1.0 nm, and ∼1.6 nm above the membrane, respectively. Furthermore, the real-time measurements show that the individual protomers of the CitS dimer move up and down independently. A three-state elevator model of independently operating protomers resembles the mechanism proposed for the aspartate transporter GltPh. Since CitS and GltPh are structurally unrelated, we conclude that the three-state elevators have evolved independently.
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Hou Z, Gangjee A, Matherly LH. The evolving biology of the proton‐coupled folate transporter: New insights into regulation, structure, and mechanism. FASEB J 2022; 36:e22164. [PMID: 35061292 PMCID: PMC8978580 DOI: 10.1096/fj.202101704r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/15/2021] [Accepted: 01/03/2022] [Indexed: 01/19/2023]
Abstract
The human proton‐coupled folate transporter (PCFT; SLC46A1) or hPCFT was identified in 2006 as the principal folate transporter involved in the intestinal absorption of dietary folates. A rare autosomal recessive hereditary folate malabsorption syndrome is attributable to human SLC46A1 variants. The recognition that hPCFT was highly expressed in many tumors stimulated substantial interest in its potential for cytotoxic drug targeting, taking advantage of its high‐level transport activity under acidic pH conditions that characterize many tumors and its modest expression in most normal tissues. To better understand the basis for variations in hPCFT levels between tissues including human tumors, studies have examined the transcriptional regulation of hPCFT including the roles of CpG hypermethylation and critical transcription factors and cis elements. Additional focus involved identifying key structural and functional determinants of hPCFT transport that, combined with homology models based on structural homologies to the bacterial transporters GlpT and LacY, have enabled new structural and mechanistic insights. Recently, cryo‐electron microscopy structures of chicken PCFT in a substrate‐free state and in complex with the antifolate pemetrexed were reported, providing further structural insights into determinants of (anti)folate recognition and the mechanism of pH‐regulated (anti)folate transport by PCFT. Like many major facilitator proteins, hPCFT exists as a homo‐oligomer, and evidence suggests that homo‐oligomerization of hPCFT monomeric proteins may be important for its intracellular trafficking and/or transport function. Better understanding of the structure, function and regulation of hPCFT should facilitate the rational development of new therapeutic strategies for conditions associated with folate deficiency, as well as cancer.
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Affiliation(s)
- Zhanjun Hou
- Molecular Therapeutics Program Barbara Ann Karmanos Cancer Institute Detroit Michigan USA
- Department of Oncology Wayne State University School of Medicine Detroit Michigan USA
| | - Aleem Gangjee
- Division of Medicinal Chemistry Graduate School of Pharmaceutical Sciences Duquesne University Pittsburgh Pennsylvania USA
| | - Larry H. Matherly
- Molecular Therapeutics Program Barbara Ann Karmanos Cancer Institute Detroit Michigan USA
- Department of Oncology Wayne State University School of Medicine Detroit Michigan USA
- Department of Pharmacology Wayne State University School of Medicine Detroit Michigan USA
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43
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Brindangnanam P, Sawant AR, Prashanth K, Coumar MS. Bacterial effluxome as a barrier against antimicrobial agents: structural biology aspects and drug targeting. Tissue Barriers 2021; 10:2013695. [PMID: 34957912 DOI: 10.1080/21688370.2021.2013695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Antimicrobial resistance (AMR) is fast becoming a medical crisis affecting the entire global population. The bacterial membrane is the first layer of defense for the bacteria against antimicrobial agents (AMA), specifically transporters in the membrane efflux these AMA out of the bacteria and plays a significant role in the AMR development. Understanding the structure and the functions of these efflux transporters is essential to overcome AMR. This review discusses efflux transporters (primary, secondary, and tripartite), their domain architectures, substrate specificities, and efflux pump inhibitors (EPI). Special emphasis on nosocomial ESKAPEE (Enterococcus faecium., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp. and Escherichia coli) pathogens, their multidrug efflux targets and inhibitors are discussed. Deep knowledge about the functioning of efflux pumps and their structural aspects will open up opportunities for developing new EPI, which could be used along with AMA as combination therapy to overcome the emerging AMR crisis.
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Affiliation(s)
- Pownraj Brindangnanam
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Ajit Ramesh Sawant
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - K Prashanth
- Department of Biotechnology, School of Life Sciences, Pondicherry University, Pondicherry, India
| | - Mohane Selvaraj Coumar
- Department of Bioinformatics, School of Life Sciences, Pondicherry University, Pondicherry, India
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Bazzone A, Tesmer L, Kurt D, Kaback HR, Fendler K, Madej MG. Investigation of sugar binding kinetics of the E. coli sugar/H + symporter XylE using solid supported membrane-based electrophysiology. J Biol Chem 2021; 298:101505. [PMID: 34929170 PMCID: PMC8784342 DOI: 10.1016/j.jbc.2021.101505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 12/11/2021] [Accepted: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
Bacterial transporters are difficult to study using conventional electrophysiology because of their low transport rates and the small size of bacterial cells. Here, we applied solid-supported membrane–based electrophysiology to derive kinetic parameters of sugar translocation by the Escherichia coli xylose permease (XylE), including functionally relevant mutants. Many aspects of the fucose permease (FucP) and lactose permease (LacY) have also been investigated, which allow for more comprehensive conclusions regarding the mechanism of sugar translocation by transporters of the major facilitator superfamily. In all three of these symporters, we observed sugar binding and transport in real time to determine KM, Vmax, KD, and kobs values for different sugar substrates. KD and kobs values were attainable because of a conserved sugar-induced electrogenic conformational transition within these transporters. We also analyzed interactions between the residues in the available X-ray sugar/H+ symporter structures obtained with different bound sugars. We found that different sugars induce different conformational states, possibly correlating with different charge displacements in the electrophysiological assay upon sugar binding. Finally, we found that mutations in XylE altered the kinetics of glucose binding and transport, as Q175 and L297 are necessary for uncoupling H+ and d-glucose translocation. Based on the rates for the electrogenic conformational transition upon sugar binding (>300 s−1) and for sugar translocation (2 s−1 − 30 s−1 for different substrates), we propose a multiple-step mechanism and postulate an energy profile for sugar translocation. We also suggest a mechanism by which d-glucose can act as an inhibitor for XylE.
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Affiliation(s)
- Andre Bazzone
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - Laura Tesmer
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - Derya Kurt
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - H Ronald Kaback
- University of California, Department of Physiology and Department of Microbiology, Immunology, Molecular Genetics, Molecular Biology Institute in Los Angeles CA, USA
| | - Klaus Fendler
- Max-Planck-Institute of Biophysics, Department of Biophysical Chemistry in Frankfurt/M, Germany
| | - M Gregor Madej
- Institute of Biophysics and Biophysical Chemistry, Department of Structural Biology, University of Regensburg, Universitätsstr. 31, 95053 Regensburg, Germany; Institute of Biophysics, Department of Structural Biology, Saarland University, Center of Human and Molecular Biology, Building 60, 66421 Homburg, Germany
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45
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Marić P, Ahel M, Maraković N, Lončar J, Mihaljević I, Smital T. Selective interaction of microcystin congeners with zebrafish (Danio rerio) Oatp1d1 transporter. CHEMOSPHERE 2021; 283:131155. [PMID: 34182632 DOI: 10.1016/j.chemosphere.2021.131155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 06/06/2021] [Accepted: 06/08/2021] [Indexed: 06/13/2023]
Abstract
Microcystins (MCs) are the most studied cyanotoxins. The uptake of MCs in cells and tissues of mammals and fish species is mostly mediated by organic anion-transporting polypeptides (OATPs in humans and rodents; Oatps in other species), and the Oatp1d1 appears to be a major transporter for MCs in fish. In this study, six MC congeners of varying physicochemical properties (MC-LR, -RR, -YR, -LW, -LF, -LA) were tested by measuring their effect on the uptake of model Oatp1d1 fluorescent substrate Lucifer yellow (LY) in HEK293T cells transiently or stably overexpressing zebrafish Oatp1d1. MC-LW and -LF showed the strongest interaction resulting in an almost complete inhibition of LY transport with IC50 values of 0.21 and 0.26 μM, while congeners -LR, -YR and -LA showed lower inhibitory effects. To discern between Oatp1d1 substrates and inhibitors, results were complemented by Michaelis-Menten kinetics and chemical analytical determinations of MCs uptake, along with molecular docking studies performed using the developed zebrafish Oatp1d1 homology model. Our study showed that Oatp1d1-mediated transport of MCs could be largely dependent on their basic physicochemical properties, with log POW being the most obvious determinant. Finally, apart from determination of the chemical composition of cynobacterial blooms, a reliable risk assessment should take into account the interaction of identified MC congeners with Oatp1d1 as their primary transporter, and herewith we demonstrated that such a comprehensive approach could be based on the use of highly specific in vitro models, accompanied by chemical assessment and in silico molecular docking studies.
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Affiliation(s)
- Petra Marić
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Marijan Ahel
- Laboratory for Analytical Chemistry and Biogeochemistry of Organic Compounds, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Nikola Maraković
- Institute for Medical Research and Occupational Health, Ksaverska Cesta 2, 10000, Zagreb, Croatia
| | - Jovica Lončar
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Ivan Mihaljević
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Tvrtko Smital
- Laboratory for Molecular Ecotoxicology, Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia.
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46
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Singh G, Akhter Y. Molecular insights into the differential efflux mechanism of Rv1634 protein, a multidrug transporter of major facilitator superfamily in Mycobacterium tuberculosis. Proteins 2021; 90:566-578. [PMID: 34601761 DOI: 10.1002/prot.26253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/20/2021] [Accepted: 09/27/2021] [Indexed: 11/08/2022]
Abstract
Currently, multidrug-resistant tuberculosis (MDR-TB) is a public health crisis and a major health security threat globally. In Mycobacterium tuberculosis (Mtb), major facilitator superfamily (MFS) is the largest group of secondary active transporters. Along with the transport of their natural substrates, MFS proteins were involved in a drug efflux mechanism that ultimately lead to resistance against available anti-TB drugs in Mtb. In the present study, the three-dimensional structure model of an MFS protein, Rv1634, a probable multidrug transporter from Mtb, was generated using homology modeling. The protein structure model was found in inward-open conformation having 14 transmembrane helices. In addition, a central transport channel was deduced across the protein, and a single binding pocket was identified halfway through the central cavity by structural alignment with the homologous protein structures. Further, Rv1634 protein was studied based on the differential structural behavior of apo and ligand-bound forms. All the protein systems were inserted into a phospholipid bilayer to characterize the conformational dynamics of the protein using molecular dynamics (MD) simulations. Detailed analysis of the MD trajectories showed the diverse substrate specificity of the binding pocket for the antibiotics that caused differential movement in the ciprofloxacin and norfloxacin, to which Mtb strains have now become resistant. The expulsion of the drugs outside the bacterial cell occurs through the alternating-access mechanism of N and C-terminal domains, which is intriguing and essential to the understanding the drug resistance mechanism in pathogenic bacteria.
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Affiliation(s)
- Garima Singh
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
| | - Yusuf Akhter
- Department of Biotechnology, Babasaheb Bhimrao Ambedkar University, Lucknow, Uttar Pradesh, India
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47
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Markham KJ, Tikhonova EB, Scarpa AC, Hariharan P, Katsube S, Guan L. Complete cysteine-scanning mutagenesis of the Salmonella typhimurium melibiose permease. J Biol Chem 2021; 297:101090. [PMID: 34416232 PMCID: PMC8437787 DOI: 10.1016/j.jbc.2021.101090] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 08/10/2021] [Accepted: 08/16/2021] [Indexed: 11/15/2022] Open
Abstract
The melibiose permease of Salmonella typhimurium (MelBSt) catalyzes the stoichiometric symport of galactopyranoside with a cation (H+, Li+, or Na+) and is a prototype for Na+-coupled major facilitator superfamily (MFS) transporters presenting from bacteria to mammals. X-ray crystal structures of MelBSt have revealed the molecular recognition mechanism for sugar binding; however, understanding of the cation site and symport mechanism is still vague. To further investigate the transport mechanism and conformational dynamics of MelBSt, we generated a complete single-Cys library containing 476 unique mutants by placing a Cys at each position on a functional Cys-less background. Surprisingly, 105 mutants (22%) exhibit poor transport activities (<15% of Cys-less transport), although the expression levels of most mutants were comparable to that of the control. The affected positions are distributed throughout the protein. Helices I and X and transmembrane residues Asp and Tyr are most affected by cysteine replacement, while helix IX, the cytoplasmic middle-loop, and C-terminal tail are least affected. Single-Cys replacements at the major sugar-binding positions (K18, D19, D124, W128, R149, and W342) or at positions important for cation binding (D55, N58, D59, and T121) abolished the Na+-coupled active transport, as expected. We mapped 50 loss-of-function mutants outside of these substrate-binding sites that suffered from defects in protein expression/stability or conformational dynamics. This complete Cys-scanning mutagenesis study indicates that MelBSt is highly susceptible to single-Cys mutations, and this library will be a useful tool for further structural and functional studies to gain insights into the cation-coupled symport mechanism for Na+-coupled MFS transporters.
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Affiliation(s)
- Kelsey J Markham
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Elena B Tikhonova
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Aaron C Scarpa
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Parameswaran Hariharan
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Satoshi Katsube
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA
| | - Lan Guan
- Department of Cell Physiology & Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, School of Medicine, Lubbock, Texas, USA.
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48
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Zhang L, Yao D, Xia Y, Zhou F, Zhang Q, Wang Q, Qin A, Zhao J, Li D, Li Y, Zhou L, Cao Y. The structural basis for glycerol permeation by human AQP7. Sci Bull (Beijing) 2021; 66:1550-1558. [PMID: 36654284 DOI: 10.1016/j.scib.2020.12.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 11/03/2020] [Accepted: 11/09/2020] [Indexed: 02/03/2023]
Abstract
Human glycerol channel aquaporin 7 (AQP7) conducts glycerol release from adipocyte and enters the cells in pancreatic islets, muscles, and kidney tubules, and thus regulates glycerol metabolism in those tissues. Compared with other human aquaglyceroporins, AQP7 shows a less conserved "NPA" motif in the center cavity and a pair of aromatic residues at Ar/R selectivity filter. To understand the structural basis for the glycerol conductance, we crystallized the human AQP7 and determined the structure at 3.7 Å. A substrate binding pocket was found near the Ar/R filter where a glycerol molecule is bound and stabilized by R229. Glycerol uptake assay on human AQP7 as well as AQP3 and AQP10 demonstrated strong glycerol transportation activities at the physiological condition. The human AQP7 structure, in combination with the molecular dynamics simulation thereon, reveals a fully closed conformation with its permeation pathway strictly confined by the Ar/R filter at the exoplasmic side and the gate at the cytoplasmic side, and the binding of glycerol at the Ar/R filter plays a critical role in controlling the glycerol flux by driving the dislocation of the residues at narrowest parts of glycerol pathway in AQP7.
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Affiliation(s)
- Li Zhang
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Deqiang Yao
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; iHuman Institute, ShanghaiTech University, Shanghai 201210, China
| | - Ying Xia
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Fu Zhou
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Qing Zhang
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Qian Wang
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China
| | - An Qin
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Jie Zhao
- Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Dianfan Li
- CAS Center for Excellence on Molecular Cell Science, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200433, China.
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 200433, China.
| | - Yu Cao
- Institute of Precision Medicine, The Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200125, China; Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China.
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49
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Guan L, Hariharan P. X-ray crystallography reveals molecular recognition mechanism for sugar binding in a melibiose transporter MelB. Commun Biol 2021; 4:931. [PMID: 34341464 PMCID: PMC8329300 DOI: 10.1038/s42003-021-02462-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 07/07/2021] [Indexed: 12/15/2022] Open
Abstract
Major facilitator superfamily_2 transporters are widely found from bacteria to mammals. The melibiose transporter MelB, which catalyzes melibiose symport with either Na+, Li+, or H+, is a prototype of the Na+-coupled MFS transporters, but its sugar recognition mechanism has been a long-unsolved puzzle. Two high-resolution X-ray crystal structures of a Salmonella typhimurium MelB mutant with a bound ligand, either nitrophenyl-α-d-galactoside or dodecyl-β-d-melibioside, were refined to a resolution of 3.05 or 3.15 Å, respectively. In the substrate-binding site, the interaction of both galactosyl moieties on the two ligands with MelBSt are virturally same, so the sugar specificity determinant pocket can be recognized, and hence the molecular recognition mechanism for sugar binding in MelB has been deciphered. The conserved cation-binding pocket is also proposed, which directly connects to the sugar specificity pocket. These key structural findings have laid a solid foundation for our understanding of the cooperative binding and symport mechanisms in Na+-coupled MFS transporters, including eukaryotic transporters such as MFSD2A. Guan and Hariharan report two crystal structures of melibiose transporter MelB in complex with substrate analogs, nitrophenyl-galactoside, and dodecyl-melibioside. Both structures revealed similar specific site for sugar recognition and resolved the cation-binding pocket, advancing the understanding of MelB and related transporters.
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Affiliation(s)
- Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA.
| | - Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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50
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Ortiz-Hernández ML, Gama-Martínez Y, Fernández-López M, Castrejón-Godínez ML, Encarnación S, Tovar-Sánchez E, Salazar E, Rodríguez A, Mussali-Galante P. Transcriptomic analysis of Burkholderia cenocepacia CEIB S5-2 during methyl parathion degradation. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:42414-42431. [PMID: 33813711 DOI: 10.1007/s11356-021-13647-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Methyl parathion (MP) is a highly toxic organophosphorus pesticide associated with water, soil, and air pollution events. The identification and characterization of microorganisms capable of biodegrading pollutants are an important environmental task for bioremediation of pesticide impacted sites. The strain Burkholderia cenocepacia CEIB S5-2 is a bacterium capable of efficiently hydrolyzing MP and biodegrade p-nitrophenol (PNP), the main MP hydrolysis product. Due to the high PNP toxicity over microbial living forms, the reports on bacterial PNP biodegradation are scarce. According to the genomic data, the MP- and PNP-degrading ability observed in B. cenocepacia CEIB S5-2 is related to the presence of the methyl parathion-degrading gene (mpd) and the gene cluster pnpABA'E1E2FDC, which include the genes implicated in the PNP degradation. In this work, the transcriptomic analysis of the strain in the presence of MP revealed the differential expression of 257 genes, including all genes implicated in the PNP degradation, as well as a set of genes related to the sensing of environmental changes, the response to stress, and the degradation of aromatic compounds, such as translational regulators, membrane transporters, efflux pumps, and oxidative stress response genes. These findings suggest that these genes play an important role in the defense against toxic effects derived from the MP and PNP exposure. Therefore, B. cenocepacia CEIB S5-2 has a great potential for application in pesticide bioremediation approaches due to its biodegradation capabilities and the differential expression of genes for resistance to MP and PNP.
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Affiliation(s)
- Ma Laura Ortiz-Hernández
- Misión Sustentabilidad México A.C., Priv. Laureles 6, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Yitzel Gama-Martínez
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México
| | - Maikel Fernández-López
- Centro de Investigación en Dinámica Celular, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - María Luisa Castrejón-Godínez
- Facultad de Ciencias Biológicas, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - Sergio Encarnación
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Efraín Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P 62209, Cuernavaca, Morelos, México
| | - Emmanuel Salazar
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Av. Universidad s/n, Col. Chamilpa, C.P 62210, Cuernavaca, Morelos, México
| | - Alexis Rodríguez
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México.
| | - Patricia Mussali-Galante
- Centro de Investigación en Biotecnología, Laboratorio de Investigaciones Ambientales, Universidad Autónoma del Estado de Morelos, Av. Universidad 1001, Col. Chamilpa, C.P. 62209, Cuernavaca, Morelos, México.
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