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Kumar S, Athreya A, Gulati A, Nair RM, Mahendran I, Ranjan R, Penmatsa A. Structural basis of inhibition of a transporter from Staphylococcus aureus, NorC, through a single-domain camelid antibody. Commun Biol 2021; 4:836. [PMID: 34226658 PMCID: PMC8257674 DOI: 10.1038/s42003-021-02357-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/10/2021] [Indexed: 12/11/2022] Open
Abstract
Transporters play vital roles in acquiring antimicrobial resistance among pathogenic bacteria. In this study, we report the X-ray structure of NorC, a 14-transmembrane major facilitator superfamily member that is implicated in fluoroquinolone resistance in drug-resistant Staphylococcus aureus strains, at a resolution of 3.6 Å. The NorC structure was determined in complex with a single-domain camelid antibody that interacts at the extracellular face of the transporter and stabilizes it in an outward-open conformation. The complementarity determining regions of the antibody enter and block solvent access to the interior of the vestibule, thereby inhibiting alternating-access. NorC specifically interacts with an organic cation, tetraphenylphosphonium, although it does not demonstrate an ability to transport it. The interaction is compromised in the presence of NorC-antibody complex, consequently establishing a strategy to detect and block NorC and related transporters through the use of single-domain camelid antibodies.
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Affiliation(s)
- Sushant Kumar
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Van Andel Institute, Grand Rapids, MI, USA
| | - Arunabh Athreya
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Ashutosh Gulati
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Rahul Mony Nair
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Ithayaraja Mahendran
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
- Structural Parasitology Lab, International Centre for Genetic engineering and Biotechnology, New Delhi, India
| | - Rakesh Ranjan
- Principal Scientist, ICAR-National Research Centre of Camel (NRCC), Bikaner, India
| | - Aravind Penmatsa
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.
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Van Campenhout R, Muyldermans S, Vinken M, Devoogdt N, De Groof TW. Therapeutic Nanobodies Targeting Cell Plasma Membrane Transport Proteins: A High-Risk/High-Gain Endeavor. Biomolecules 2021; 11:63. [PMID: 33418902 PMCID: PMC7825061 DOI: 10.3390/biom11010063] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/30/2020] [Accepted: 01/01/2021] [Indexed: 02/06/2023] Open
Abstract
Cell plasma membrane proteins are considered as gatekeepers of the cell and play a major role in regulating various processes. Transport proteins constitute a subclass of cell plasma membrane proteins enabling the exchange of molecules and ions between the extracellular environment and the cytosol. A plethora of human pathologies are associated with the altered expression or dysfunction of cell plasma membrane transport proteins, making them interesting therapeutic drug targets. However, the search for therapeutics is challenging, since many drug candidates targeting cell plasma membrane proteins fail in (pre)clinical testing due to inadequate selectivity, specificity, potency or stability. These latter characteristics are met by nanobodies, which potentially renders them eligible therapeutics targeting cell plasma membrane proteins. Therefore, a therapeutic nanobody-based strategy seems a valid approach to target and modulate the activity of cell plasma membrane transport proteins. This review paper focuses on methodologies to generate cell plasma membrane transport protein-targeting nanobodies, and the advantages and pitfalls while generating these small antibody-derivatives, and discusses several therapeutic nanobodies directed towards transmembrane proteins, including channels and pores, adenosine triphosphate-powered pumps and porters.
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Affiliation(s)
- Raf Van Campenhout
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (R.V.C.); (M.V.)
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium;
| | - Mathieu Vinken
- Department of In Vitro Toxicology and Dermato-Cosmetology, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium; (R.V.C.); (M.V.)
| | - Nick Devoogdt
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium;
| | - Timo W.M. De Groof
- In Vivo Cellular and Molecular Imaging Laboratory, Vrije Universiteit Brussel, Laarbeeklaan 103, 1090 Brussels, Belgium;
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Medrano-Soto A, Ghazi F, Hendargo KJ, Moreno-Hagelsieb G, Myers S, Saier MH. Expansion of the Transporter-Opsin-G protein-coupled receptor superfamily with five new protein families. PLoS One 2020; 15:e0231085. [PMID: 32320418 PMCID: PMC7176098 DOI: 10.1371/journal.pone.0231085] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/17/2020] [Indexed: 02/06/2023] Open
Abstract
Here we provide bioinformatic evidence that the Organo-Arsenical Exporter (ArsP), Endoplasmic Reticulum Retention Receptor (KDELR), Mitochondrial Pyruvate Carrier (MPC), L-Alanine Exporter (AlaE), and the Lipid-linked Sugar Translocase (LST) protein families are members of the Transporter-Opsin-G Protein-coupled Receptor (TOG) Superfamily. These families share domains homologous to well-established TOG superfamily members, and their topologies of transmembranal segments (TMSs) are compatible with the basic 4-TMS repeat unit characteristic of this Superfamily. These repeat units tend to occur twice in proteins as a result of intragenic duplication events, often with subsequent gain/loss of TMSs in many superfamily members. Transporters within the ArsP family allow microbial pathogens to expel toxic arsenic compounds from the cell. Members of the KDELR family are involved in the selective retrieval of proteins that reside in the endoplasmic reticulum. Proteins of the MPC family are involved in the transport of pyruvate into mitochondria, providing the organelle with a major oxidative fuel. Members of family AlaE excrete L-alanine from the cell. Members of the LST family are involved in the translocation of lipid-linked glucose across the membrane. These five families substantially expand the range of substrates of transport carriers in the superfamily, although KDEL receptors have no known transport function. Clustering of protein sequences reveals the relationships among families, and the resulting tree correlates well with the degrees of sequence similarity documented between families. The analyses and programs developed to detect distant relatedness, provide insights into the structural, functional, and evolutionary relationships that exist between families of the TOG superfamily, and should be of value to many other investigators.
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Affiliation(s)
- Arturo Medrano-Soto
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Faezeh Ghazi
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Kevin J. Hendargo
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | | | - Scott Myers
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
| | - Milton H. Saier
- Department of Molecular Biology, Division of Biological Sciences, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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Wang D, Liu H, Wang H, Zhang P, Shi C. A novel sucrose transporter gene IbSUT4 involves in plant growth and response to abiotic stress through the ABF-dependent ABA signaling pathway in Sweetpotato. BMC Plant Biol 2020; 20:157. [PMID: 32293270 PMCID: PMC7157994 DOI: 10.1186/s12870-020-02382-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 04/02/2020] [Indexed: 05/23/2023]
Abstract
BACKGROUND To maintain sweetpotato (Ipomoea batatas (L.) Lam) growth and yield, sucrose must be transported from the leaves to the roots. Sucrose transporters or carriers (SUTs or SUCs) transport sucrose and are involved in plant growth and response to abiotic stress. However, the mechanisms of SUTs in sweetpotato abiotic stress resistance remains to be determined. RESULTS In the present study, we cloned a novel IbSUT4 gene; the protein encoded by this gene is localized in the tonoplast and plasma membrane. The plant growth was promoted in the IbSUT4 transgenic Arabidopsis thaliana lines, with increased expression of AtFT, a regulator of flowering time in plants. Over-expression of IbSUT4 in Arabidopsis thaliana resulted in higher sucrose content in the roots and lower sucrose content in the leaves, as compared to the wild-type (WT) plants, leading to improved stress tolerance during seedling growth. Moreover, we systematically analyzed the mechanisms of IbSUT4 in response to abiotic stress. The results suggest that the ABRE-motif was localized in the IbSUT4 promoter region, and the expression of the ABA signaling pathway genes (i.e., ABF2, ABF4, SnRK2.2, SnRK2.3, and PYL8/RCAR3) were induced, and the expression of ABI1 was inhibited. CONCLUSIONS Our dates provide evidence that IbSUT4 is not only involved in plant growth but also is an important positive regulator in plant stress tolerance through the ABF-dependent ABA signaling pathway.
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Affiliation(s)
- Dandan Wang
- State Key Laboratory of Crop Biology, College of Agronomic Science, Shandong Agricultural University, Tai' an, 271018, China
| | - Hongjuan Liu
- State Key Laboratory of Crop Biology, College of Agronomic Science, Shandong Agricultural University, Tai' an, 271018, China
| | - Hongxia Wang
- National Key of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of sciences, Shanghai, 200032, China
| | - Peng Zhang
- National Key of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of sciences, Shanghai, 200032, China
| | - Chunyu Shi
- State Key Laboratory of Crop Biology, College of Agronomic Science, Shandong Agricultural University, Tai' an, 271018, China.
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Jiang S, Balan B, Assis RDAB, Sagawa CHD, Wan X, Han S, Wang L, Zhang L, Zaini PA, Walawage SL, Jacobson A, Lee SH, Moreira LM, Leslie CA, Dandekar AM. Genome-Wide Profiling and Phylogenetic Analysis of the SWEET Sugar Transporter Gene Family in Walnut and Their Lack of Responsiveness to Xanthomonas arboricola pv. juglandis Infection. Int J Mol Sci 2020; 21:ijms21041251. [PMID: 32070009 PMCID: PMC7072939 DOI: 10.3390/ijms21041251] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/12/2022] Open
Abstract
Following photosynthesis, sucrose is translocated to sink organs, where it provides the primary source of carbon and energy to sustain plant growth and development. Sugar transporters from the SWEET (sugar will eventually be exported transporter) family are rate-limiting factors that mediate sucrose transport across concentration gradients, sustain yields, and participate in reproductive development, plant senescence, stress responses, as well as support plant-pathogen interaction, the focus of this study. We identified 25 SWEET genes in the walnut genome and distinguished each by its individual gene structure and pattern of expression in different walnut tissues. Their chromosomal locations, cis-acting motifs within their 5' regulatory elements, and phylogenetic relationship patterns provided the first comprehensive analysis of the SWEET gene family of sugar transporters in walnut. This family is divided into four clades, the analysis of which suggests duplication and expansion of the SWEET gene family in Juglans regia. In addition, tissue-specific gene expression signatures suggest diverse possible functions for JrSWEET genes. Although these are commonly used by pathogens to harness sugar products from their plant hosts, little was known about their role during Xanthomonas arboricola pv. juglandis (Xaj) infection. We monitored the expression profiles of the JrSWEET genes in different tissues of "Chandler" walnuts when challenged with pathogen Xaj417 and concluded that SWEET-mediated sugar translocation from the host is not a trigger for walnut blight disease development. This may be directly related to the absence of type III secretion system-dependent transcription activator-like effectors (TALEs) in Xaj417, which suggests different strategies are employed by this pathogen to promote susceptibility to this major aboveground disease of walnuts.
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Affiliation(s)
- Shijiao Jiang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
- College of Life Sciences, China West Normal University, Nanchong 637000, China
| | - Bipin Balan
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
- Dipartimento di Scienze Agrarie Alimentari Forestali, Università di Palermo, Viale delle Scienze Ed. 4, 90128 Palermo, Italy
| | - Renata de A. B. Assis
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Cintia H. D. Sagawa
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Xueqin Wan
- Department of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.W.); (S.H.)
| | - Shan Han
- Department of Forestry, Sichuan Agricultural University, Chengdu 611130, China; (X.W.); (S.H.)
| | - Le Wang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Lanlan Zhang
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
- Department of Horticulture, College of Agriculture and Food Science, Zhejiang A&F University, Lin’an, Hangzhou 311300, China
| | - Paulo A. Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Sriema L. Walawage
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Aaron Jacobson
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Steven H. Lee
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Leandro M. Moreira
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto 35400-000, Brazil;
| | - Charles A. Leslie
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
| | - Abhaya M. Dandekar
- Department of Plant Sciences, University of California, Davis, CA 95616, USA; (S.J.); (B.B.); (R.d.A.B.A.); (C.H.D.S.); (L.W.); (L.Z.); (P.A.Z.); (S.L.W.); (A.J.); (S.H.L.); (C.A.L.)
- Correspondence:
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Diehn TA, Bienert MD, Pommerrenig B, Liu Z, Spitzer C, Bernhardt N, Fuge J, Bieber A, Richet N, Chaumont F, Bienert GP. Boron demanding tissues of Brassica napus express specific sets of functional Nodulin26-like Intrinsic Proteins and BOR1 transporters. Plant J 2019; 100:68-82. [PMID: 31148338 PMCID: PMC6852077 DOI: 10.1111/tpj.14428] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 05/01/2019] [Accepted: 05/28/2019] [Indexed: 05/22/2023]
Abstract
The sophisticated uptake and translocation regulation of the essential element boron (B) in plants is ensured by two transmembrane transporter families: the Nodulin26-like Intrinsic Protein (NIP) and BOR transporter family. Though the agriculturally important crop Brassica napus is highly sensitive to B deficiency, and NIPs and BORs have been suggested to be responsible for B efficiency in this species, functional information of these transporter subfamilies is extremely rare. Here, we molecularly characterized the NIP and BOR1 transporter family in the European winter-type cv. Darmor-PBY018. Our transport assays in the heterologous oocyte and yeast expression systems as well as in growth complementation assays in planta demonstrated B transport activity of NIP5, NIP6, NIP7 and BOR1 isoforms. Moreover, we provided functional and quantitative evidence that also members of the NIP2, NIP3 and NIP4 groups facilitate the transport of B. A detailed B- and tissue-dependent B-transporter expression map was generated by quantitative polymerase chain reaction. We showed that NIP5 isoforms are highly upregulated under B-deficient conditions in roots, but also in shoot tissues. Moreover, we detected transcripts of several B-permeable NIPs from various groups in floral tissues that contribute to the B distribution within the highly B deficiency-sensitive flowers.
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Affiliation(s)
- Till Arvid Diehn
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Manuela Désirée Bienert
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Benjamin Pommerrenig
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
- Division of Plant PhysiologyUniversity KaiserslauternKaiserslautern67663Germany
| | - Zhaojun Liu
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Christoph Spitzer
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Nadine Bernhardt
- Experimental Taxonomy, Genebank DepartmentLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Jacqueline Fuge
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Annett Bieber
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
| | - Nicolas Richet
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - François Chaumont
- Louvain Institute of Biomolecular Science and TechnologyUCLouvainLouvain‐la‐Neuve1348Belgium
| | - Gerd Patrick Bienert
- Metalloid Transport, Department of Physiology and Cell BiologyLeibniz Institute of Plant Genetics and Crop Plant Research (IPK)Gatersleben06466Germany
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7
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Wang L, Yao L, Hao X, Li N, Qian W, Yue C, Ding C, Zeng J, Yang Y, Wang X. Tea plant SWEET transporters: expression profiling, sugar transport, and the involvement of CsSWEET16 in modifying cold tolerance in Arabidopsis. Plant Mol Biol 2018; 96:577-592. [PMID: 29616437 DOI: 10.1007/s11103-018-0716-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 03/06/2018] [Indexed: 05/18/2023]
Abstract
Thirteen SWEET transporters were identified in Camellia sinensis and the cold-suppression gene CsSWEET16 contributed to sugar compartmentation across the vacuole and function in modifying cold tolerance in Arabidopsis. The sugars will eventually be exported transporters (SWEET) family of sugar transporters in plants is a recently identified protein family of sugar uniporters that contain seven transmembrane helices harbouring two MtN3 motifs. SWEETs play important roles in various biological processes, including plant responses to environmental stimuli. In this study, 13 SWEET transporters were identified in Camellia sinensis and were divided into four clades. Transcript abundances of CsSWEET genes were detected in various tissues. CsSWEET1a/1b/2a/2b/2c/3/9b/16/17 were expressed in all of the selected tissues, whereas the expression of CsSWEET5/7/9a/15 was not detected in some tissues, including those of mature leaves. Expression analysis of nine CsSWEET genes in leaves in response to abiotic stresses, natural cold acclimation and Colletotrichum camelliae infection revealed that eight CsSWEET genes responded to abiotic stress, while CsSWEET3 responded to C. camelliae infection. Functional analysis of 13 CsSWEET activities in yeast revealed that CsSWEET1a/1b/7/17 exhibit transport activity for glucose analogues and other types of hexose molecules. Further characterization of the cold-suppression gene CsSWEET16 revealed that this gene is localized in the vacuolar membrane. CsSWEET16 contributed to sugar compartmentation across the vacuole and function in modifying cold tolerance in Arabidopsis. Together, these findings demonstrate that CsSWEET genes play important roles in the response to abiotic and biotic stresses in tea plants and provide insights into the characteristics of SWEET genes in tea plants, which could serve as the basis for further functional identification of such genes.
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Affiliation(s)
- Lu Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Lina Yao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
| | - Xinyuan Hao
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Nana Li
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
| | - Wenjun Qian
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
| | - Chuan Yue
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
| | - Changqing Ding
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
| | - Jianming Zeng
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China
| | - Yajun Yang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China.
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China.
| | - Xinchao Wang
- National Center for Tea Plant Improvement, Tea Research Institute, Chinese Academy of Agricultural Sciences, 9th South of Meiling Road, Hangzhou, 310008, China.
- Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Hangzhou, 310008, China.
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8
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Guefrachi I, Pierre O, Timchenko T, Alunni B, Barrière Q, Czernic P, Villaécija-Aguilar JA, Verly C, Bourge M, Fardoux J, Mars M, Kondorosi E, Giraud E, Mergaert P. Bradyrhizobium BclA Is a Peptide Transporter Required for Bacterial Differentiation in Symbiosis with Aeschynomene Legumes. Mol Plant Microbe Interact 2015; 28:1155-66. [PMID: 26106901 DOI: 10.1094/mpmi-04-15-0094-r] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Nodules of legume plants are highly integrated symbiotic systems shaped by millions of years of evolution. They harbor nitrogen-fixing rhizobium bacteria called bacteroids. Several legume species produce peptides called nodule-specific cysteine-rich (NCR) peptides in the symbiotic nodule cells which house the bacteroids. NCR peptides are related to antimicrobial peptides of innate immunity. They induce the endosymbionts into a differentiated, enlarged, and polyploid state. The bacterial symbionts, on their side, evolved functions for the response to the NCR peptides. Here, we identified the bclA gene of Bradyrhizobium sp. strains ORS278 and ORS285, which is required for the formation of differentiated and functional bacteroids in the nodules of the NCR peptide-producing Aeschynomene legumes. The BclA ABC transporter promotes the import of NCR peptides and provides protection against the antimicrobial activity of these peptides. Moreover, BclA can complement the role of the related BacA transporter of Sinorhizobium meliloti, which has a similar symbiotic function in the interaction with Medicago legumes.
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Affiliation(s)
- Ibtissem Guefrachi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Olivier Pierre
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Tatiana Timchenko
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Benoît Alunni
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Quentin Barrière
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Pierre Czernic
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | | | - Camille Verly
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Mickaël Bourge
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
| | - Joël Fardoux
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Mohamed Mars
- 2 Research Unit Biodiversity & Valorization of Arid Areas Bioressources (BVBAA), Faculty of Sciences, Gabès, Tunisia
| | - Eva Kondorosi
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
- 4 Institute of Biochemistry, Hungarian Academy of Sciences, Biological Research Centre, Szeged, Hungary
| | - Eric Giraud
- 3 Laboratoire des Symbioses Tropicales et Méditerranéennes, Institut pour la Recherche et le Développement, UMR IRD/SupAgro/INRA/UM2/CIRAD, Montpellier, France
| | - Peter Mergaert
- 1 Institute for Integrative Biology of the Cell, UMR 9198, CNRS/Université Paris-Sud/CEA, Gif-sur-Yvette, France
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9
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Suzuki M, Sato Y, Wu S, Kang BH, McCarty DR. Conserved Functions of the MATE Transporter BIG EMBRYO1 in Regulation of Lateral Organ Size and Initiation Rate. Plant Cell 2015; 27:2288-300. [PMID: 26276834 PMCID: PMC4568504 DOI: 10.1105/tpc.15.00290] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 07/06/2015] [Accepted: 07/23/2015] [Indexed: 05/18/2023]
Abstract
Genetic networks that determine rates of organ initiation and organ size are key regulators of plant architecture. Whereas several genes that influence the timing of lateral organ initiation have been identified, the regulatory pathways in which these genes operate are poorly understood. Here, we identify a class of genes implicated in regulation of the lateral organ initiation rate. Loss-of-function mutations in the MATE transporter encoded by maize (Zea mays) Big embryo 1 (Bige1) cause accelerated leaf and root initiation as well as enlargement of the embryo scutellum. BIGE1 is localized to trans-Golgi, indicating a possible role in secretion of a signaling molecule. Interestingly, phenotypes of bige1 bear striking similarity to cyp78a mutants identified in diverse plant species. We show that a CYP78A gene is upregulated in bige1 mutant embryos, suggesting a role for BIGE1 in feedback regulation of a CYP78A pathway. We demonstrate that accelerated leaf formation and early flowering phenotypes conditioned by mutants of Arabidopsis thaliana BIGE1 orthologs are complemented by maize Bige1, showing that the BIGE1 transporter has a conserved function in regulation of lateral organ initiation in plants. We propose that BIGE1 is required for transport of an intermediate or product associated with the CYP78A pathway.
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Affiliation(s)
- Masaharu Suzuki
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Yutaka Sato
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shan Wu
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
| | - Byung-Ho Kang
- Department of Microbiology and Cell Science, University of Florida, Gainesville, Florida 32611
| | - Donald R McCarty
- Plant Molecular and Cellular Biology Program, Horticultural Sciences Department, University of Florida, Gainesville, Florida 32611
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10
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Huang Q, Vera Delgado JM, Seni Pinoargote OD, Llaguno RA. Molecular evolution of the Slc15 family and its response to waterborne copper and mercury exposure in tilapia. Aquat Toxicol 2015; 163:140-147. [PMID: 25897688 DOI: 10.1016/j.aquatox.2015.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 06/04/2023]
Abstract
The solute carrier 15 family (Slc15), also called oligopeptide transporter family (Pept), was well-known for its role in the cellular uptake of di/tripeptides and peptide-like molecules. Our understanding of Slc15 family has already been enlarged since the rapid increasing of genome information; however, efforts are still expected to reveal the diversification of the family in an evolutionary manner. In the study, the sequence information were collected and analyzed through eleven eukaryotic organism representatives, especially in fish species. Gene expansion was observed through the evolution of the family. Further study was carried out with the representative species-Nile tilapia (Oreochromis niloticus). Tissue expression profiles were compared among members of the Slc15 family. Generally, they were all highly expressed both in the intestine and stomach, however, different members possessed its special tissue expression pattern. The mRNA levels of all the members (except Slc15a4) decreased after fasting while refeeding could restore the expression level. The recovery ability was impaired after exposure to environmental relevant concentration of copper (Cu(2+), 160 nmol/L). By contrast, mercury (Hg(2+), 25 nmol/L) did not exert significant impact on the recovery ability.
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Affiliation(s)
- Qiansheng Huang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China; Instituto de Investigación, Universidad Técnica de Manabí, Portoviejo, Ecuador; Proyecto Prometeo - Secretaría de Educación Superior, Ciencia, Tecnología e Innovación (SENESCYT), Quito, Ecuador.
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11
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Straub D, Ludewig U, Neuhäuser B. A nitrogen-dependent switch in the high affinity ammonium transport in Medicago truncatula. Plant Mol Biol 2014; 86:485-94. [PMID: 25164101 DOI: 10.1007/s11103-014-0243-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 08/18/2014] [Indexed: 05/26/2023]
Abstract
Ammonium transporters (AMTs) are crucial for the high affinity primary uptake and translocation of ammonium in plants. In the model legume Medicago truncatula, the genomic set of AMT-type ammonium transporters comprises eight members. Only four genes were abundantly expressed in young seedlings, both in roots and shoots. While the expression of all AMTs in the shoot was not affected by the nitrogen availability, the dominating MtAMT1;1 gene was repressed by nitrogen in roots, despite that cellular nitrogen concentrations were far above deficiency levels. A contrasting de-repression by nitrogen was observed for MtAMT1;4 and MtAMT2;1, which were both expressed at intermediate level. Weak expression was found for MtAMT1;2 and MtAMT2;3, while the other AMTs were not detected in young seedlings. When expressed from their endogenous promoters, translational fusion proteins of MtAMT1;1 and MtAMT2;1 with green fluorescent protein were co-localized in the plasma membrane of rhizodermal cells, but also detected in cortical root layers. Both transporter proteins similarly functionally complemented a yeast strain that is deficient in high affinity ammonium transport, both at acidic and neutral pH. The uptake into yeast mediated by these transporters saturated with Km AMT1;1 = 89 µM and Km AMT2;1 = 123 µM, respectively. When expressed in oocytes, MtAMT1;1 mediated much larger (15)N-ammonium uptake than MtAMT2;1, but NH4 (+) currents were only recorded for MtAMT1;1. These currents saturated with a voltage-dependent Km = 90 µM at -80 mV. The cellular localization and regulation of the AMTs suggests that MtAMT1;1 encodes the major high affinity ammonium transporter gene in low nitrogen grown young M. truncatula roots and despite the similar localization and substrate affinity, MtAMT2;1 appears functionally distinct and more important at higher nitrogen supply.
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Affiliation(s)
- Daniel Straub
- Institute of Crop Science, Nutritional Crop Physiology, University of Hohenheim, Fruwirthstr. 20, 70593, Stuttgart, Germany
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12
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13
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Zdrazil B, Chichester C, Zander Balderud L, Engkvist O, Gaulton A, Overington JP. Transporter assays and assay ontologies: useful tools for drug discovery. Drug Discov Today Technol 2014; 12:e47-e54. [PMID: 25027375 DOI: 10.1016/j.ddtec.2014.03.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Transport proteins represent an eminent class of drug targets and ADMET (absorption, distribution, metabolism, excretion, toxicity) associated genes. There exists a large number of distinct activity assays for transport proteins, depending on not only the measurement needed (e.g. transport activity, strength of ligand–protein interaction), but also due to heterogeneous assay setups used by different research groups. Efforts to systematically organize this (divergent) bioassay data have large potential impact in Public-Private partnership and conventional commercial drug discovery. In this short review, we highlight some of the frequently used high-throughput assays for transport proteins, and we discuss emerging assay ontologies and their application to this field. Focusing on human P-glycoprotein (Multidrug resistance protein 1; gene name: ABCB1, MDR1), we exemplify how annotation of bioassay data per target class could improve and add to existing ontologies, and we propose to include an additional layer of metadata supporting data fusion across different bioassays.
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Affiliation(s)
- Barbara Zdrazil
- University of Vienna, Division of Drug Design and Medicinal Chemistry, Department of Pharmaceutical Chemistry, Pharmacoinformatics Research Group, Althanstrasse 14, A-1090 Vienna, Austria
| | - Christine Chichester
- Swiss Institute of Bioinformatics, CALIPHO Group, CMU - Rue Michel-Servet 1, 1211 Geneva 4, Switzerland
| | | | - Ola Engkvist
- Discovery Sciences, Chemistry Innovation Center, AstraZeneca R&D, Mölndal, Sweden
| | - Anna Gaulton
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
| | - John P Overington
- European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom
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14
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Viereck M, Gaulton A, Digles D, Ecker GF. Transporter taxonomy - a comparison of different transport protein classification schemes. Drug Discov Today Technol 2014; 12:e37-e46. [PMID: 25027374 DOI: 10.1016/j.ddtec.2014.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Currently, there are more than 800 well characterized human membrane transport proteins (including channels and transporters) and there are estimates that about 10% (approx. 2000) of all human genes are related to transport. Membrane transport proteins are of interest as potential drug targets, for drug delivery, and as a cause of side effects and drug–drug interactions. In light of the development of Open PHACTS, which provides an open pharmacological space, we analyzed selected membrane transport protein classification schemes (Transporter Classification Database, ChEMBL, IUPHAR/BPS Guide to Pharmacology, and Gene Ontology) for their ability to serve as a basis for pharmacology driven protein classification. A comparison of these membrane transport protein classification schemes by using a set of clinically relevant transporters as use-case reveals the strengths and weaknesses of the different taxonomy approaches.
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Affiliation(s)
- Michael Viereck
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Anna Gaulton
- European Molecular Biology Laboratory ©?? European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Daniela Digles
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
| | - Gerhard F Ecker
- University of Vienna, Department of Pharmaceutical Chemistry, Althanstrasse 14, 1090 Vienna, Austria
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15
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Cai SY, Mennone A, Soroka CJ, Boyer JL. Altered expression and function of canalicular transporters during early development of cholestatic liver injury in Abcb4-deficient mice. Am J Physiol Gastrointest Liver Physiol 2014; 306:G670-6. [PMID: 24481602 PMCID: PMC3989703 DOI: 10.1152/ajpgi.00334.2013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 01/23/2014] [Indexed: 01/31/2023]
Abstract
Deficiency of ABCB4 is associated with several forms of cholestasis in humans. Abcb4(-/-) mice also develop cholestasis, but it remains uncertain what role other canalicular transporters play in the development of this disease. We examined the expression of these transporters in Abcb4(-/-) mice compared with their wild-type littermate controls at ages of 10 days and 3, 6, and 12 wk. Elevated plasma bile acid levels were already detected at 10 days and at all ages thereafter in Abcb4(-/-) mice. The expression of Bsep, Mrp2, Atp8b1, Abcg5, and Abcg8 liver proteins did not change at 10 days, but Bsep, Mrp2, and Atp8b1 were reduced, whereas Abcg5 and Abcg8 expression were increased in Abcb4(-/-) mice at all later ages. Lower bile acid concentrations were also detected in the bile of 6-wk-old Abcb4(-/-) mice. Immunofluorescence labeling revealed distorted canalicular architecture in the liver tissue by 12 wk in Abcb4(-/-) mice. Whereas Bsep and Mrp2 remained associated with the apical membrane, Atp8b1 was now localized in discrete punctuate structures adjacent to the canalicular membrane in these mice. Expression of Bsep mRNA was increased in the livers of 10-day-old Abcb4(-/-) mice, whereas Ost-α was decreased. By 12 wk, Bsep, Mrp2, and Abcg5 mRNA were all increased, whereas Ost-α and Ntcp were reduced. These findings indicate that canalicular transporters that determine the formation of bile are altered early in the development of cholestasis in Abcb4(-/-) mice and may contribute to the pathogenesis of cholestasis in this disorder.
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Affiliation(s)
- Shi-Ying Cai
- Department of Internal Medicine and Yale Liver Center, Yale University School of Medicine, New Haven, Connecticut
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16
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Degnan PH, Barry NA, Mok KC, Taga ME, Goodman AL. Human gut microbes use multiple transporters to distinguish vitamin B₁₂ analogs and compete in the gut. Cell Host Microbe 2014; 15:47-57. [PMID: 24439897 PMCID: PMC3923405 DOI: 10.1016/j.chom.2013.12.007] [Citation(s) in RCA: 182] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 11/13/2013] [Accepted: 12/18/2013] [Indexed: 12/20/2022]
Abstract
Genomic and metagenomic sequencing efforts, including human microbiome projects, reveal that microbes often encode multiple systems that appear to accomplish the same task. Whether these predictions reflect actual functional redundancies is unclear. We report that the prominent human gut symbiont Bacteroides thetaiotaomicron employs three functional, homologous vitamin B₁₂ transporters that in at least two cases confer a competitive advantage in the presence of distinct B₁₂ analogs (corrinoids). In the mammalian gut, microbial fitness can be determined by the presence or absence of a single transporter. The total number of distinct corrinoid transporter families in the human gut microbiome likely exceeds those observed in B. thetaiotaomicron by an order of magnitude. These results demonstrate that human gut microbes use elaborate mechanisms to capture and differentiate corrinoids in vivo and that apparent redundancies observed in these genomes can instead reflect hidden specificities that determine whether a microbe will colonize its host.
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Affiliation(s)
- Patrick H Degnan
- Department of Microbial Pathogenesis and Microbial Diversity Institute, Yale University, New Haven, CT 06536, USA
| | - Natasha A Barry
- Department of Microbial Pathogenesis and Microbial Diversity Institute, Yale University, New Haven, CT 06536, USA
| | - Kenny C Mok
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Michiko E Taga
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Andrew L Goodman
- Department of Microbial Pathogenesis and Microbial Diversity Institute, Yale University, New Haven, CT 06536, USA.
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17
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Abstract
Some unicellular organisms can take up urea from the surrounding fluids by an uphill pumping mechanism. Several active (energy-dependent) urea transporters (AUTs) have been cloned in these organisms. Functional studies show that active urea transport also occurs in elasmobranchs, amphibians, and mammals. In the two former groups, active urea transport may serve to conserve urea in body fluids in order to balance external high ambient osmolarity or prevent desiccation. In mammals, active urea transport may be associated with the need to either store and/or reuse nitrogen in the case of low nitrogen supply, or to excrete nitrogen efficiently in the case of excess nitrogen intake. There are probably two different families of AUTs, one with a high capacity able to establish only a relatively modest transepithelial concentration difference (renal tubule of some frogs, pars recta of the mammalian kidney, early inner medullary collecting duct in some mammals eating protein-poor diets) and others with a low capacity but able to maintain a high transepithelial concentration difference that has been created by another mechanism or in another organ (elasmobranch gills, ventral skin of some toads, and maybe mammalian urinary bladder). Functional characterization of these transporters shows that some are coupled to sodium (symports or antiports) while others are sodium-independent. In humans, only one genetic anomaly, with a mild phenotype (familial azotemia), is suspected to concern one of these transporters. In spite of abundant functional evidence for such transporters in higher organisms, none have been molecularly identified yet.
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Affiliation(s)
- Lise Bankir
- INSERM UMRS 1138, Centre de Recherche Des Cordeliers, Paris, France,
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18
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Léran S, Varala K, Boyer JC, Chiurazzi M, Crawford N, Daniel-Vedele F, David L, Dickstein R, Fernandez E, Forde B, Gassmann W, Geiger D, Gojon A, Gong JM, Halkier BA, Harris JM, Hedrich R, Limami AM, Rentsch D, Seo M, Tsay YF, Zhang M, Coruzzi G, Lacombe B. A unified nomenclature of NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER family members in plants. Trends Plant Sci 2014; 19:5-9. [PMID: 24055139 DOI: 10.1016/j.tplants.2013.08.008] [Citation(s) in RCA: 358] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/16/2013] [Accepted: 08/22/2013] [Indexed: 05/18/2023]
Abstract
Members of the plant NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER (NRT1/PTR) family display protein sequence homology with the SLC15/PepT/PTR/POT family of peptide transporters in animals. In comparison to their animal and bacterial counterparts, these plant proteins transport a wide variety of substrates: nitrate, peptides, amino acids, dicarboxylates, glucosinolates, IAA, and ABA. The phylogenetic relationship of the members of the NRT1/PTR family in 31 fully sequenced plant genomes allowed the identification of unambiguous clades, defining eight subfamilies. The phylogenetic tree was used to determine a unified nomenclature of this family named NPF, for NRT1/PTR FAMILY. We propose that the members should be named accordingly: NPFX.Y, where X denotes the subfamily and Y the individual member within the species.
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Affiliation(s)
- Sophie Léran
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France
| | - Kranthi Varala
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Jean-Christophe Boyer
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France
| | - Maurizio Chiurazzi
- Institute of Genetics and Biophysics 'Adriano Buzzati-Traverso', CNR, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Nigel Crawford
- Section of Cell and Developmental Biology, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Françoise Daniel-Vedele
- INRA AgroParisTech, UMR1318 Institut Jean-Pierre Bourgin, RD10, 78026 Versailles Cedex, France
| | - Laure David
- INRA AgroParisTech, UMR1318 Institut Jean-Pierre Bourgin, RD10, 78026 Versailles Cedex, France
| | - Rebecca Dickstein
- Department of Biological Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Emilio Fernandez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa Baja E, Campus de Rabanales, E-14071, Córdoba, Spain
| | - Brian Forde
- Centre for Sustainable Agriculture, Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Walter Gassmann
- Division of Plant Sciences, CS Bond Life Sciences Center and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA
| | - Dietmar Geiger
- Universität Würzburg, Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Alain Gojon
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France
| | - Ji-Ming Gong
- National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Barbara A Halkier
- DynaMo Centre of Excellence, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Jeanne M Harris
- Department of Plant Biology, 315 Jeffords Hall, 63 Carrigan Drive, University of Vermont, Burlington, VT 05405, USA
| | - Rainer Hedrich
- Universität Würzburg, Julius-von-Sachs-Institut für Biowissenschaften, Lehrstuhl für Molekulare Pflanzenphysiologie und Biophysik, Julius-von-Sachs-Platz 2, 97082 Würzburg, Germany
| | - Anis M Limami
- UMR 1345 Research Institute of Horticulture and Seeds (INRA, Agrocampus-Ouest, University of Angers), SFR 4207 Quasav, 2 Bd Lavoisier, 49045 Angers Cedex, France
| | - Doris Rentsch
- Institute of Plant Sciences, University of Bern, Altenbergrain 21, 3013 Bern, Switzerland
| | - Mitsunori Seo
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan
| | - Mingyong Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Gloria Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003, USA
| | - Benoît Lacombe
- Biochimie et Physiologie Moléculaire des Plantes, UMR CNRS/INRA/UM2/SupAgro, Institut de Biologie Intégrative des Plantes 'Claude Grignon', Place Viala, 34060 Montpellier, France.
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19
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Kasmati AR, Töpel M, Khan NZ, Patel R, Ling Q, Karim S, Aronsson H, Jarvis P. Evolutionary, molecular and genetic analyses of Tic22 homologues in Arabidopsis thaliana chloroplasts. PLoS One 2013; 8:e63863. [PMID: 23675512 PMCID: PMC3652856 DOI: 10.1371/journal.pone.0063863] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 04/05/2013] [Indexed: 11/18/2022] Open
Abstract
The Tic22 protein was previously identified in pea as a putative component of the chloroplast protein import apparatus. It is a peripheral protein of the inner envelope membrane, residing in the intermembrane space. In Arabidopsis, there are two Tic22 homologues, termed atTic22-III and atTic22-IV, both of which are predicted to localize in chloroplasts. These two proteins defined clades that are conserved in all land plants, which appear to have evolved at a similar rates since their separation >400 million years ago, suggesting functional conservation. The atTIC22-IV gene was expressed several-fold more highly than atTIC22-III, but the genes exhibited similar expression profiles and were expressed throughout development. Knockout mutants lacking atTic22-IV were visibly normal, whereas those lacking atTic22-III exhibited moderate chlorosis. Double mutants lacking both isoforms were more strongly chlorotic, particularly during early development, but were viable and fertile. Double-mutant chloroplasts were small and under-developed relative to those in wild type, and displayed inefficient import of precursor proteins. The data indicate that the two Tic22 isoforms act redundantly in chloroplast protein import, and that their function is non-essential but nonetheless required for normal chloroplast biogenesis, particularly during early plant development.
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Affiliation(s)
- Ali Reza Kasmati
- University of Leicester, Department of Biology, Leicester, United Kingdom
| | - Mats Töpel
- University of Leicester, Department of Biology, Leicester, United Kingdom
| | - Nadir Zaman Khan
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg, Sweden
| | - Ramesh Patel
- University of Leicester, Department of Biology, Leicester, United Kingdom
| | - Qihua Ling
- University of Leicester, Department of Biology, Leicester, United Kingdom
| | - Sazzad Karim
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg, Sweden
| | - Henrik Aronsson
- University of Gothenburg, Department of Biological and Environmental Sciences, Gothenburg, Sweden
| | - Paul Jarvis
- University of Leicester, Department of Biology, Leicester, United Kingdom
- * E-mail:
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Chauton MS, Winge P, Brembu T, Vadstein O, Bones AM. Gene regulation of carbon fixation, storage, and utilization in the diatom Phaeodactylum tricornutum acclimated to light/dark cycles. Plant Physiol 2013; 161:1034-48. [PMID: 23209127 PMCID: PMC3561001 DOI: 10.1104/pp.112.206177] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The regulation of carbon metabolism in the diatom Phaeodactylum tricornutum at the cell, metabolite, and gene expression levels in exponential fed-batch cultures is reported. Transcriptional profiles and cell chemistry sampled simultaneously at all time points provide a comprehensive data set on carbon incorporation, fate, and regulation. An increase in Nile Red fluorescence (a proxy for cellular neutral lipids) was observed throughout the light period, and water-soluble glucans increased rapidly in the light period. A near-linear decline in both glucans and lipids was observed during the dark period, and transcription profile data indicated that this decline was associated with the onset of mitosis. More than 4,500 transcripts that were differentially regulated during the light/dark cycle are identified, many of which were associated with carbohydrate and lipid metabolism. Genes not previously described in algae and their regulation in response to light were integrated in this analysis together with proposed roles in metabolic processes. Some very fast light-responding genes in, for example, fatty acid biosynthesis were identified and allocated to biosynthetic processes. Transcripts and cell chemistry data reflect the link between light energy availability and light energy-consuming metabolic processes. Our data confirm the spatial localization of processes in carbon metabolism to either plastids or mitochondria or to glycolysis/gluconeogenesis, which are localized to the cytosol, chloroplast, and mitochondria. Localization and diel expression pattern may be of help to determine the roles of different isoenzymes and the mining of genes involved in light responses and circadian rhythms.
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21
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Abstract
Photosynthesis in marine diatoms is a vital fraction of global primary production empowered by CO(2)-concentrating mechanisms. Acquisition of HCO(3)(-) from seawater is a critical primary step of the CO(2)-concentrating mechanism, allowing marine photoautotrophic eukaryotes to overcome CO(2) limitation in alkaline high-salinity water. However, little is known about molecular mechanisms governing this process. Here, we show the importance of a plasma membrane-type HCO(3)(-) transporter for CO(2) acquisition in a marine diatom. Ten putative solute carrier (SLC) family HCO(3)(-) transporter genes were found in the genome of the marine pennate diatom Phaeodactylum tricornutum. Homologs also exist in marine centric species, Thalassiosira pseudonana, suggesting a general occurrence of SLC transporters in marine diatoms. Seven genes were found to encode putative mammalian-type SLC4 family transporters in P. tricornutum, and three of seven genes were specifically transcribed under low CO(2) conditions. One of these gene products, PtSLC4-2, was localized at the plasmalemma and significantly stimulated both dissolved inorganic carbon (DIC) uptake and photosynthesis in P. tricornutum. DIC uptake by PtSLC4-2 was efficiently inhibited by an anion-exchanger inhibitor, 4,4'-diisothiocyanostilbene-2,2'-disulfonic acid, in a concentration-dependent manner and highly dependent on Na(+) ions at concentrations over 100 mM. These results show that DIC influx into marine diatoms is directly driven at the plasmalemma by a specific HCO(3)(-) transporter with a significant halophilic nature.
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Affiliation(s)
- Kensuke Nakajima
- Research Centre for Environmental Bioscience, Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
| | | | - Yusuke Matsuda
- Research Centre for Environmental Bioscience, Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, Sanda, Hyogo 669-1337, Japan
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22
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Chan CW, Spathis R, Reiff DM, McGrath SE, Garruto RM, Lum JK. Diversity of Plasmodium falciparum chloroquine resistance transporter (pfcrt) exon 2 haplotypes in the Pacific from 1959 to 1979. PLoS One 2012; 7:e30213. [PMID: 22272308 PMCID: PMC3260253 DOI: 10.1371/journal.pone.0030213] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Accepted: 12/13/2011] [Indexed: 12/03/2022] Open
Abstract
Nearly one million deaths are attributed to malaria every year. Recent reports of multi-drug treatment failure of falciparum malaria underscore the need to understand the molecular basis of drug resistance. Multiple mutations in the Plasmodium falciparum chloroquine resistance transporter (pfcrt) are involved in chloroquine resistance, but the evolution of complex haplotypes is not yet well understood. Using over 4,500 archival human serum specimens collected from 19 Pacific populations between 1959 and 1979, the period including and just prior to the appearance of chloroquine treatment failure in the Pacific, we PCR-amplified and sequenced a portion of the pfcrt exon 2 from 771 P. falciparum-infected individuals to explore the spatial and temporal variation in falciparum malaria prevalence and the evolution of chloroquine resistance. In the Pacific, the prevalence of P. falciparum varied considerably across ecological zones. On the island of New Guinea, the decreases in prevalence of P. falciparum in coastal, high-transmission areas over time were contrasted by the increase in prevalence during the same period in the highlands, where transmission was intermittent. We found 78 unique pfcrt haplotypes consisting of 34 amino acid substitutions and 28 synonymous mutations. More importantly, two pfcrt mutations (N75D and K76T) implicated in chloroquine resistance were present in parasites from New Hebrides (now Vanuatu) eight years before the first report of treatment failure. Our results also revealed unexpectedly high levels of genetic diversity in pfcrt exon 2 prior to the historical chloroquine resistance selective sweep, particularly in areas where disease burden was relatively low. In the Pacific, parasite genetic isolation, as well as host acquired immune status and genetic resistance to malaria, were important contributors to the evolution of chloroquine resistance in P. falciparum.
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Affiliation(s)
- Chim W Chan
- Laboratory of Evolutionary Anthropology and Health, Binghamton University, Binghamton, New York, United States of America.
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23
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Gupta AB, Verma RK, Agarwal V, Vajpai M, Bansal V, Sankararamakrishnan R. MIPModDB: a central resource for the superfamily of major intrinsic proteins. Nucleic Acids Res 2012; 40:D362-9. [PMID: 22080560 PMCID: PMC3245135 DOI: 10.1093/nar/gkr914] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 10/05/2011] [Accepted: 10/08/2011] [Indexed: 12/23/2022] Open
Abstract
The channel proteins belonging to the major intrinsic proteins (MIP) superfamily are diverse and are found in all forms of life. Water-transporting aquaporin and glycerol-specific aquaglyceroporin are the prototype members of the MIP superfamily. MIPs have also been shown to transport other neutral molecules and gases across the membrane. They have internal homology and possess conserved sequence motifs. By analyzing a large number of publicly available genome sequences, we have identified more than 1000 MIPs from diverse organisms. We have developed a database MIPModDB which will be a unified resource for all MIPs. For each MIP entry, this database contains information about the source, gene structure, sequence features, substitutions in the conserved NPA motifs, structural model, the residues forming the selectivity filter and channel radius profile. For selected set of MIPs, it is possible to derive structure-based sequence alignment and evolutionary relationship. Sequences and structures of selected MIPs can be downloaded from MIPModDB database which is freely available at http://bioinfo.iitk.ac.in/MIPModDB.
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Affiliation(s)
- Anjali Bansal Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 and Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ravi Kumar Verma
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 and Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Vatsal Agarwal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 and Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Manu Vajpai
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 and Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Vivek Bansal
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 and Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
| | - Ramasubbu Sankararamakrishnan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016 and Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, India
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Abstract
The accumulation of silicon (Si) differs greatly with plant species and cultivars due to different ability of the roots to take up Si. In Si accumulating plants such as rice, barley and maize, Si uptake is mediated by the influx (Lsi1) and efflux (Lsi2) transporters. Here we report isolation and functional analysis of two Si efflux transporters (CmLsi2-1 and CmLsi2-2) from two pumpkin (Cucurbita moschata Duch.) cultivars contrasting in Si uptake. These cultivars are used for rootstocks of bloom and bloomless cucumber, respectively. Different from mutations in the Si influx transporter CmLsi1, there was no difference in the sequence of either CmLsi2 between two cultivars. Both CmLsi2-1 and CmLsi2-2 showed an efflux transport activity for Si and they were expressed in both the roots and shoots. These results confirm our previous finding that mutation in CmLsi1, but not in CmLsi2-1 and CmLsi2-2 are responsible for bloomless phenotype resulting from low Si uptake.
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Affiliation(s)
- Namiki Mitani-Ueno
- Institute of Plant Science and Resources, Okayama University, Chuo, Kurashiki, Japan
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Carrie C, Murcha MW, Whelan J. An in silico analysis of the mitochondrial protein import apparatus of plants. BMC Plant Biol 2010; 10:249. [PMID: 21078193 PMCID: PMC3095331 DOI: 10.1186/1471-2229-10-249] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Accepted: 11/16/2010] [Indexed: 05/04/2023]
Abstract
BACKGROUND An in silico analysis of the mitochondrial protein import apparatus from a variety of species; including Chlamydomonas reinhardtii, Chlorella variabilis, Ectocarpus siliculosus, Cyanidioschyzon merolae, Physcomitrella patens, Selaginella moellendorffii, Picea glauca, Oryza sativa and Arabidopsis thaliana was undertaken to determine if components differed within and between plant and non-plant species. RESULTS The channel forming subunits of the outer membrane components Tom40 and Sam50 are conserved between plant groups and other eukaryotes. In contrast, the receptor component(s) in green plants, particularly Tom20, (C. reinhardtii, C. variabilis, P. patens, S. moellendorffii, P. glauca, O. sativa and A. thaliana) are specific to this lineage. Red algae contain a Tom22 receptor that is orthologous to yeast Tom22. Furthermore, plant mitochondrial receptors display differences between various plant lineages. These are evidenced by distinctive motifs in all plant Metaxins, which are absent in red algae, and the presence of the outer membrane receptor OM64 in Angiosperms (rice and Arabidopsis), but not in lycophytes (S. moellendorffii) and gymnosperms (P. glauca). Furthermore, although the intermembrane space receptor Mia40 is conserved across a wide phylogenetic range, its function differs between lineages. In all plant lineages, Tim17 contains a C-terminal extension, which may act as a receptor component for the import of nucleic acids into plant mitochondria. CONCLUSIONS It is proposed that the observed functional divergences are due to the selective pressure to sort proteins between mitochondria and chloroplasts, resulting in differences in protein receptor components between plant groups and other organisms. Additionally, diversity of receptor components is observed within the plant kingdom. Even when receptor components are orthologous across plant and non-plant species, it appears that the functions of these have expanded or diverged in a lineage specific manner.
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Affiliation(s)
- Chris Carrie
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling, Crawley 6009, WA, Australia
| | - Monika W Murcha
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling, Crawley 6009, WA, Australia
| | - James Whelan
- Australian Research Council Centre of Excellence in Plant Energy Biology, University of Western Australia, 35 Stirling, Crawley 6009, WA, Australia
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Afoufa-Bastien D, Medici A, Jeauffre J, Coutos-Thévenot P, Lemoine R, Atanassova R, Laloi M. The Vitis vinifera sugar transporter gene family: phylogenetic overview and macroarray expression profiling. BMC Plant Biol 2010; 10:245. [PMID: 21073695 PMCID: PMC3095327 DOI: 10.1186/1471-2229-10-245] [Citation(s) in RCA: 123] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Accepted: 11/12/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND In higher plants, sugars are not only nutrients but also important signal molecules. They are distributed through the plant via sugar transporters, which are involved not only in sugar long-distance transport via the loading and the unloading of the conducting complex, but also in sugar allocation into source and sink cells. The availability of the recently released grapevine genome sequence offers the opportunity to identify sucrose and monosaccharide transporter gene families in a woody species and to compare them with those of the herbaceous Arabidopsis thaliana using a phylogenetic analysis. RESULTS In grapevine, one of the most economically important fruit crop in the world, it appeared that sucrose and monosaccharide transporter genes are present in 4 and 59 loci, respectively and that the monosaccharide transporter family can be divided into 7 subfamilies. Phylogenetic analysis of protein sequences has indicated that orthologs exist between Vitis and Arabidospis. A search for cis-regulatory elements in the promoter sequences of the most characterized transporter gene families (sucrose, hexoses and polyols transporters), has revealed that some of them might probably be regulated by sugars. To profile several genes simultaneously, we created a macroarray bearing cDNA fragments specific to 20 sugar transporter genes. This macroarray analysis has revealed that two hexose (VvHT1, VvHT3), one polyol (VvPMT5) and one sucrose (VvSUC27) transporter genes, are highly expressed in most vegetative organs. The expression of one hexose transporter (VvHT2) and two tonoplastic monosaccharide transporter (VvTMT1, VvTMT2) genes are regulated during berry development. Finally, three putative hexose transporter genes show a preferential organ specificity being highly expressed in seeds (VvHT3, VvHT5), in roots (VvHT2) or in mature leaves (VvHT5). CONCLUSIONS This study provides an exhaustive survey of sugar transporter genes in Vitis vinifera and revealed that sugar transporter gene families in this woody plant are strongly comparable to those of herbaceous species. Dedicated macroarrays have provided a Vitis sugar transporter genes expression profiling, which will likely contribute to understand their physiological functions in plant and berry development. The present results might also have a significant impact on our knowledge on plant sugar transporters.
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Affiliation(s)
- Damien Afoufa-Bastien
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
| | - Anna Medici
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
| | - Julien Jeauffre
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
- UMR Génétique et Horticulture (GenHort) - INRA/INH/UA - BP 60057 - 49071 Beaucouzé cedex, France
| | - Pierre Coutos-Thévenot
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
| | - Rémi Lemoine
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
| | - Rossitza Atanassova
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
| | - Maryse Laloi
- UMR-CNRS-UP 6503 - LACCO - Laboratoire de Catalyse en Chimie Organique - Equipe Physiologie Moléculaire du Transport de Sucres - Université de Poitiers - Bâtiment Botanique - 40 Avenue du Recteur Pineau, 86022 Poitiers cedex, France
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Abstract
The ability to take up and metabolize glucose at the cellular level is a property shared by the vast majority of existing organisms. Most mammalian cells import glucose by a process of facilitative diffusion mediated by members of the Glut (SLC2A) family of membrane transport proteins. Fourteen Glut proteins are expressed in the human and they include transporters for substrates other than glucose, including fructose, myoinositol, and urate. The primary physiological substrates for at least half of the 14 Glut proteins are either uncertain or unknown. The well-established glucose transporter isoforms, Gluts 1-4, are known to have distinct regulatory and/or kinetic properties that reflect their specific roles in cellular and whole body glucose homeostasis. Separate review articles on many of the Glut proteins have recently appeared in this journal. Here, we provide a very brief summary of the known properties of the 14 Glut proteins and suggest some avenues of future investigation in this area.
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Affiliation(s)
- Bernard Thorens
- Department of Physiology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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28
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Kong Y, Zhou G, Avci U, Gu X, Jones C, Yin Y, Xu Y, Hahn MG. Two poplar glycosyltransferase genes, PdGATL1.1 and PdGATL1.2, are functional orthologs to PARVUS/AtGATL1 in Arabidopsis. Mol Plant 2009; 2:1040-50. [PMID: 19825678 DOI: 10.1093/mp/ssp068] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Several genes in Arabidopsis, including PARVUS/AtGATL1, have been implicated in xylan synthesis. However, the biosynthesis of xylan in woody plants, where this polysaccharide is a major component of wood, is poorly understood. Here, we characterize two Populus genes, PdGATL1.1 and PdGATL1.2, the closest orthologs to the Arabidopsis PARVUS/GATL1 gene, with respect to their gene expression in poplar, their sub-cellular localization, and their ability to complement the parvus mutation in Arabidopsis. Overexpression of the two poplar genes in the parvus mutant rescued most of the defects caused by the parvus mutation, including morphological changes, collapsed xylem, and altered cell wall monosaccharide composition. Quantitative RT-PCR showed that PdGATL1.1 is expressed most strongly in developing xylem of poplar. In contrast, PdGATL1.2 is expressed much more uniformly in leaf, shoot tip, cortex, phloem, and xylem, and the transcript level of PdGATL1.2 is much lower than that of PdGATL1.1 in all tissues examined. Sub-cellular localization experiments showed that these two proteins are localized to both ER and Golgi in comparison with marker proteins resident to these sub-cellular compartments. Our data indicate that PdGATL1.1 and PdGATL1.2 are functional orthologs of PARVUS/GATL1 and can play a role in xylan synthesis, but may also have role(s) in the synthesis of other wall polymers.
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Affiliation(s)
- Yingzhen Kong
- Complex Carbohydrate Research Center, The University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
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29
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Abstract
Silicon exerts beneficial effects on plant growth and production by alleviating both biotic and abiotic stresses including diseases, pests, lodging, drought, and nutrient imbalance. Recently, two genes (Lsi1 and Lsi2) encoding Si transporters have been identified from rice. Lsi1 (low silicon 1) belongs to a Nod26-like major intrinsic protein subfamily in aquaporin, while Lsi2 encodes a putative anion transporter. Lsi1 is localized on the distal side of both exodermis and endodermis in rice roots, while Lsi2 is localized on the proximal side of the same cells. Lsi1 shows influx transport activity for Si, while Lsi2 shows efflux transport activity. Therefore, Lsi1 is responsible for transport of Si from the external solution to the root cells, whereas Lsi2 is an efflux transporter responsible for the transport of Si from the root cells to the apoplast. Coupling of Lsi1 with Lsi2 is required for efficient uptake of Si in rice.
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Affiliation(s)
- J F Ma
- Research Institute for Bioresources, Okayama University, Chuo 2-20-1, Kurashiki, Japan.
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30
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Anzai N. [Membrane transport proteins: update]. Nihon Jinzo Gakkai Shi 2008; 50:110-113. [PMID: 18421966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
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31
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Sun AJ, Xu HL, Gong WK, Zhai HL, Meng K, Wang YQ, Wei XL, Xiao GF, Zhu Z. Cloning and expression analysis of rice sucrose transporter genes OsSUT2M and OsSUT5Z. J Integr Plant Biol 2008; 50:62-75. [PMID: 18666953 DOI: 10.1111/j.1744-7909.2007.00596.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Two sucrose transporter (SUT) cDNAs, OsSUT2M and OsSUT5Z, were isolated from rice (Oryza sativa L.) by reverse transcription polymerase chain reaction (RT-PCR). Sequencing results indicate they are 1,531 bp and 1,635 bp in length including complete open reading frame 1,506 bp and 1,608 bp, which encode 502 amino acids and 536 amino acids, respectively. The TopPred program suggested that both sucrose transporter proteins, OsSUT2M and OsSUT5Z, consist of potentially 12 transmembrane domains. Semi-quantitative RT-PCR was carried out to investigate the gene expression patterns of OsSUT2M and OsSUT5Z. In vegetative organs, transcripts of OsSUT2M were higher in source leaf blades than in other organs at the same development stage, whereas transcripts of OsSUT5Z were less traceable in all organs investigated. In reproductive organs, both transcripts of these two genes were high in panicles from the booting stage to 7 days after flowering (DAF) and then sharply declined. The potential physiology functions of these two sucrose transporters are discussed.
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Affiliation(s)
- Ai-Jun Sun
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, the Chinese Academy of Sciences, Beijing 100101, China
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32
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Yang ZJ, Zhou JP, Li GR, Zhang Y, Ren ZL. [Cloning and expression of Gymnadenia conopsea GcSec61beta gene encoding endosplasmic reticulum membrane translocation channel protein]. Zhi Wu Sheng Li Yu Fen Zi Sheng Wu Xue Xue Bao 2007; 33:354-60. [PMID: 17675760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Protein translocation channel in endosplasmic reticulum (ER) of eukaryotes is composed of several subunits of Sec61 complex, which is essential for protein secretion. In the present study, we cloned a full-length cDNA fragment of 621 bp coding 107 amino acids from a psychrophile and endangered plant Gymnadenia conopsea, which grows in high land. Sequence analysis revealed that the gene was highly homologous to the member Sec61beta of ER protein transporter channel, which was thus designated as GcSec61beta. Phylogenetic tree shows that the GcSec61beta was closely related to the corresponding genes from Arabidopsis thaliana and Oryza sativa. Results of semi-quantitative RT-PCR showed that the expression of GcSec61beta was high both in leaves and the bud, and also induced by low temperature treatment. The sequence of the GcSec61beta was introduced into pET28a vector and transformed to E. coli strain BL21. The growth of E. coli was slowed down but the cold resistance was increased by the expression of GcSec61beta, which provides a new function of GcSec61beta protein.
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Affiliation(s)
- Zu-Jun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China.
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33
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Abstract
Sucrose is the primary product of photosynthetic CO(2) fixation that is used for the distribution of assimilated carbon within higher plants. Its partitioning from the site of synthesis to different sites of storage, conversion into other storage compounds or metabolic degradation involves various steps of cell-to-cell movement and transport. Many of these steps occur within symplastic domains, i.e. sucrose moves passively cell-to-cell through plasmodesmata. Some essential steps, however, occur between symplastically isolated cells or tissues. In these cases, sucrose is transiently released into the apoplast and its cell-to-cell transport depends on the activity of plasma membrane-localized, energy dependent, H(+)-symporting carrier proteins. This paper reviews the current knowledge of sucrose transporter physiology and molecular biology.
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Affiliation(s)
- Norbert Sauer
- Molekulare Pflanzenphysiologie, FAU Erlangen-Nürnberg, Staudtstrasse 5, D-91058 Erlangen, Germany.
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Nishino K. [Roles of xenobiotic transporters in bacterial drug resistance and virulence]. Nihon Rinsho 2007; 65 Suppl 2 Pt. 1:407-14. [PMID: 17455654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Kunihiko Nishino
- Institute of Scientific and Industrial Research, Osaka University
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35
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Abstract
Sequencing of plant genomes allowed the identification of various members of the mitochondrial carrier family (MCF). In plants, these structurally related proteins are involved in the transport of solutes like nucleotides, phosphate, di- and tricarboxylates across the mitochondrial membrane and therefore exhibit physiological functions similar to known isoforms from animal or yeast mitochondria. Interestingly, various studies led to the recognition of MCF proteins which mediate the transport of different substrates like folates, S-adenosylmethionine, ADPglucose or ATP, ADP and AMP in plastids.
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Affiliation(s)
- Ilka Haferkamp
- Zelluläre Physiologie/Membrantransport, Universität Kaiserslautern, D-67663 Kaiserslautern, Germany.
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36
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Abstract
TransportDB () is a comprehensive database resource of information on cytoplasmic membrane transporters and outer membrane channels in organisms whose complete genome sequences are available. The complete set of membrane transport systems and outer membrane channels of each organism are annotated based on a series of experimental and bioinformatic evidence and classified into different types and families according to their mode of transport, bioenergetics, molecular phylogeny and substrate specificities. User-friendly web interfaces are designed for easy access, query and download of the data. Features of the TransportDB website include text-based and BLAST search tools against known transporter and outer membrane channel proteins; comparison of transporter and outer membrane channel contents from different organisms; known 3D structures of transporters, and phylogenetic trees of transporter families. On individual protein pages, users can find detailed functional annotation, supporting bioinformatic evidence, protein/DNA sequences, publications and cross-referenced external online resource links. TransportDB has now been in existence for over 10 years and continues to be regularly updated with new evidence and data from newly sequenced genomes, as well as having new features added periodically.
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Affiliation(s)
| | | | - Ian T. Paulsen
- To whom correspondence should be addressed. Tel: +1 301 795 7531; Fax: +1 301 838 0208;
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37
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Abstract
BACKGROUND Two families of proteins that transport small peptides, the oligopeptide transporters (OPTs) and the peptide transporters (PTRs), have been recognized in eukaryotes. Higher plants contain a far greater number of genes for these transporters than do other eukaryotes. This may be indicative of the relative importance of (oligo)peptides and their transport to plant growth and metabolism. RECENT PROGRESS Recent studies are now allowing us to assign functions to these transporters and are starting to identify their in-planta substrates, revealing unexpected and important contributions of the transporters to plant growth and developmental processes. This Botanical Briefing appraises recent findings that PTRs and OPTs have key roles to play in the control of plant cell growth and development. Evidence is presented that some of these transporters have functions outside that of nitrogen nutrition and that these carriers can also surprise us with their totally unexpected choice of substrates.
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38
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Schreiber S, Stengel R, Westermann M, Volkmer-Engert R, Pop OI, Müller JP. Affinity of TatCd for TatAd Elucidates Its Receptor Function in the Bacillus subtilis Twin Arginine Translocation (Tat) Translocase System. J Biol Chem 2006; 281:19977-84. [PMID: 16698798 DOI: 10.1074/jbc.m513900200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Twin arginine translocation (Tat) systems catalyze the transport of folded proteins across the bacterial cytosolic membrane or the chloroplast thylakoid membrane. In the Tat systems of Escherichia coli and many other species TatA-, TatB-, and TatC-like proteins have been identified as essential translocase components. In contrast, the Bacillus subtilis phosphodiesterase PhoD-specific system consists only of a pair of TatA(d)/TatC(d) proteins and involves a TatA(d) protein engaged in a cytosolic and a membrane-embedded localization. Because soluble TatA(d) was able to bind the twin arginine signal peptide of prePhoD prior to membrane integration it could serve to recruit its substrate to the membrane via the interaction with TatC(d). By analyzing the distribution of TatA(d) and studying the mutual affinity with TatC(d) we have shown here that TatC(d) assists the membrane localization of TatA(d). Besides detergent-solubilized TatC(d), membrane-integrated TatC(d) showed affinity for soluble TatA(d). By using a peptide library-specific binding of TatA(d) to cytosolic loops of membrane protein TatC(d) was demonstrated. Depletion of TatC(d) in B. subtilis resulted in a drastic reduction of TatA(d), indicating a stabilizing effect of TatC(d) for TatA(d). In addition, the presence of the substrate prePhoD was the prerequisite for appropriate localization in the cytosolic membrane of B. subtilis as demonstrated by freeze-fracture experiments.
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Affiliation(s)
- Sandra Schreiber
- Institut für Molekulare Zellbiologie, Friedrich-Schiller-Universität Jena, Drackendorfer Strasse 1, D-07747 Jena, Germany
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39
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Abstract
Drug transporters are now increasingly recognized as important determinants of variable drug disposition and response. In addition, transporter associated problems appear to be occurring with greater frequency during the drug discovery and development process. What has not been clear is whether drug transporter related issues are a truly new problem, or whether such issues had existed all along, but were previously unrecognized or ignored. In this review, a brief overview of key drug transporters will be outlined. In addition, a commentary on specific issues of relevance to pharmaceutical sciences in terms of the role and relevance of drug transporters to the drug discovery and development process is provided.
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Affiliation(s)
- Richard B Kim
- Division of Clinical Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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40
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Abstract
Efforts to define the mechanisms governing neurotransmitter uptake and drug action have moved into high gear with the publication of a high-resolution structure of a leucine transporter from Aquifex aeolicus, a bacterial member of the SLC6 transporter family. Solved with the substrate leucine bound, the new structure corroborates extensive biochemical and mutagenesis studies performed with related mammalian neurotransmitter transporters and provides exciting suggestions as to how coupling arises between ions and substrates to permit efficient neurotransmitter clearance.
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Affiliation(s)
- L Keith Henry
- Department of Pharmacology and Center for Molecular Neuroscience, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA
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41
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Abstract
The Transporter Classification Database (TCDB) is a web accessible, curated, relational database containing sequence, classification, structural, functional and evolutionary information about transport systems from a variety of living organisms. TCDB is a curated repository for factual information compiled from >10 000 references, encompassing ∼3000 representative transporters and putative transporters, classified into >400 families. The transporter classification (TC) system is an International Union of Biochemistry and Molecular Biology approved system of nomenclature for transport protein classification. TCDB is freely accessible at . The web interface provides several different methods for accessing the data, including step-by-step access to hierarchical classification, direct search by sequence or TC number and full-text searching. The functional ontology that underlies the database structure facilitates powerful query searches that yield valuable data in a quick and easy way. The TCDB website also offers several tools specifically designed for analyzing the unique characteristics of transport proteins. TCDB not only provides curated information and a tool for classifying newly identified membrane proteins, but also serves as a genome transporter-annotation tool.
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Affiliation(s)
- Milton H Saier
- Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA.
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42
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Kiranmayi P, Mohan PM. Metal transportome of Neurospora crassa. In Silico Biol 2006; 6:169-80. [PMID: 16922681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Neurospora crassa has been the model filamentous fungus for the study of many fundamental cellular mechanisms of transport and metabolism. The recently completed genome sequence of N. crassa has over 10,000 genes without significant matches for a large number of genes (41%) in the sequence databases, indeed presents many challenges for new discoveries. Using transporter database and BLAST searches a total of 65 open reading frames for putative cation transporter genes have been identified in N. crassa. These were further confirmed by characteristic features of the family like transmembrane domains (TOPPRED 2), conserved motifs (Clustal W) and phylogenetic analysis (TREETOP). In Neurospora cation transporter genes constitute nearly 18.3% of the total membrane transport systems, which is higher than E. coli (8.8%), S. cerevisiae (13.7%), S. pombe (17.2%), A. fumigatus (10.1%), A. thaliana (16.8%) and H. sapiens (15.6%). We refer to the complete complement of metal ion transporter genes as "Metal Transportome". There are a total of 33 putative transporters for alkali and alkaline earth metals constituting 18 for calcium (P-ATPase, VIC, CaCA, Mid1), 7 for sodium (P-ATPase, CPA1, CPA2), 4 for potassium (Trk, VIC, KUP), and 4 for magnesium (MIT). Transition metal ion transporters account for 32 transporters including 7 for zinc (ZIP), 6 for copper (Ctr2, Ctr1), 2 each for manganese (Nramp), iron (OFeT), arsenite (ArsAB, ACR3) and other metal ions (ABC and P-ATPase) and 1 each for nickel (NiCoT) and chromate (CHR). N. crassa has 7 linkage groups of which LGI harbors 21 of metal ion transporters and in contrast LGVII has only 2. Studies on metal transportomes of different organisms will help to unravel the role of metal ion transporters in homeostasis.
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Affiliation(s)
- Patnala Kiranmayi
- Department of Biochemistry, Osmania University Hyderabad-500 007, India
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43
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Abstract
A structural class in the MemGen classification of membrane proteins is a set of evolutionary related proteins sharing a similar global fold. A structural class contains both closely related pairs of proteins for which homology is clear from sequence comparison and very distantly related pairs, for which it is not possible to establish homology based on sequence similarity alone. In the latter case the evolutionary link is based on hydropathy profile analysis. Here, we use these evolutionary related sets of proteins to analyze the relationship between E-values in BLAST searches, sequence similarities in multiple sequence alignments and structural similarities in hydropathy profile analyses. Two structural classes of secondary transporters termed ST[3], which includes the Ion Transporter (IT) superfamily and ST[4], which includes the DAACS family (TC# 2.A.23) were extracted from the NCBI protein database. ST[3] contains 2051 unique sequences distributed over 32 families and 59 subfamilies. ST[4] is a smaller class containing 399 unique sequences distributed over 2 families and 7 subfamilies. One subfamily in ST[4] contains a new class of binding protein dependent secondary transporters. Comparison of the averaged hydropathy profiles of the subfamilies in ST[3] and ST[4] revealed that the two classes represent different folds. Divergence of the sequences in ST[4] is much smaller than observed in ST[3], suggesting different constraints on the proteins during evolution. Analysis of the correlation between the evolutionary relationship of pairs of proteins in a class and the BLAST E-value revealed that: (i) the BLAST algorithm is unable to pick up the majority of the links between proteins in structural class ST[3], (ii) "low complexity filtering" and "composition based statistics" improve the specificity, but strongly reduce the sensitivity of BLAST searches for distantly related proteins, indicating that these filters are too stringent for the proteins analyzed, and (iii) the E-value cut-off, which may be used to evaluate evolutionary significance of a hit in a BLAST search is very different for the two structural classes of membrane proteins.
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Affiliation(s)
- Juke S Lolkema
- Molecular Microbiology, Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands.
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44
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Höglund PJ, Adzic D, Scicluna SJ, Lindblom J, Fredriksson R. The repertoire of solute carriers of family 6: Identification of new human and rodent genes. Biochem Biophys Res Commun 2005; 336:175-89. [PMID: 16125675 DOI: 10.1016/j.bbrc.2005.08.048] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2005] [Accepted: 08/05/2005] [Indexed: 11/18/2022]
Abstract
Tremendous amount of primary sequence information has been made available from the genome sequencing projects, although a complete annotation and identification of all genes is still far from being complete. Here, we present the identification of two new human genes from the pharmacologically important family of transporter proteins, solute carriers family 6 (SLC6). These were named SLC6A17 and SLC6A18 by HUGO. The human repertoire of SLC6 proteins now consists of 19 functional members and four pseudogenes. We also identified the corresponding orthologues and additional genes from mouse and rat genomes. Detailed phylogenetic analysis of the entire family of SLC6 proteins in mammals shows that this family can be divided into four subgroups. We used Hidden Markov Models for these subgroups and identified in total 430 unique SLC6 proteins from 10 animal, one plant, two fungi, and 196 bacterial genomes. It is evident that SLC6 proteins are present in both animals and bacteria, and that three of the four subfamilies of mammalian SLC6 proteins are present in Caenorhabditis elegans, showing that these subfamilies are evolutionary very ancient. Moreover, we performed tissue localization studies on the entire family of SLC6 proteins on a panel of 15 rat tissues and further, the expression of three of the new genes was studied using quantitative real-time PCR showing expression in multiple central and peripheral tissues. This paper presents an overall overview of the gene repertoire of the SLC6 gene family and its expression profile in rats.
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Affiliation(s)
- Pär J Höglund
- Department of Neuroscience, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
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45
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Abstract
The evolutionary process that transformed a cyanobacterial endosymbiont into contemporary plastids involved not only inheritance but also invention. Because gram-negative bacteria lack a system for polypeptide import, the envelope translocon complex of the general protein import pathway was the most important invention of organelle evolution resulting in a pathway to import back into plastids those nuclear-encoded proteins supplemented with a transit peptide. Genome information of cyanobacteria, phylogenetically diverse plastids, and the nuclei of the first red alga, a diatom, and Arabidopsis thaliana allows us to trace back the evolutionary origin of the twelve currently known translocon components and to partly deduce their assembly sequence. Development of the envelope translocon was initiated by recruitment of a cyanobacterial homolog of the protein-import channel Toc75, which belongs to a ubiquitous and essential family of Omp85/D15 outer membrane proteins of gram-negative bacteria that mediate biogenesis of beta-barrel proteins. Likewise, three other translocon subunits (Tic20, Tic22, and Tic55) and several stromal chaperones have been inherited from the ancestral cyanobacterium and modified to take over the novel function of precursor import. Most of the remaining subunits seem to be of eukaryotic origin, recruited from pre-existing nuclear genes. The next subunits that joined the evolving protein import complex likely were Toc34 and Tic110, as indicated by the presence of homologous genes in the red alga Cyanidioschyzon merolae, followed by the stromal processing peptidase, members of the Toc159 receptor family, Toc64, Tic40, and finally some regulatory redox components (Tic62, Tic32), all of which were probably required to increase specificity and efficiency of precursor import.
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Affiliation(s)
- Sigrun Reumann
- Albrecht-von-Haller-Institute for Plant Sciences, Department of Plant Biochemistry, Göttingen, Germany.
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46
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Keros S, Hablitz JJ. Subtype-Specific GABA Transporter Antagonists Synergistically Modulate Phasic and Tonic GABAA Conductances in Rat Neocortex. J Neurophysiol 2005; 94:2073-85. [PMID: 15987761 DOI: 10.1152/jn.00520.2005] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
GABAergic inhibition in the brain can be classified as either phasic or tonic. γ-Aminobutyric acid (GABA) uptake by GABA transporters (GATs) can limit the time course of phasic currents arising from endogenous and exogenous GABA, as well as decrease a tonically active GABA current. GABA transporter subtypes 1 and 3 (GAT-1 and GAT-3) are the most heavily expressed of the four known GAT subtypes. The role of GATs in shaping GABA currents in the neocortex has not been explored. We obtained patch-clamp recordings from layer II/III pyramidal cells and layer I interneurons in rat sensorimotor cortex. We found that selective GAT-1 inhibition with NO711 decreased the amplitude and increased the decay time of evoked inhibitory postsynaptic currents (IPSCs) but had no effect on the tonic current or spontaneous IPSCs (sIPSCs). GAT-2/3 inhibition with SNAP-5114 had no effect on IPSCs or the tonic current. Coapplication of NO711 and SNAP-5114 substantially increased tonic currents and synergistically decreased IPSC amplitudes and increased IPSC decay times. sIPSCs were not resolvable with coapplication of NO711 and SNAP-5114. The effects of the nonselective GAT antagonist nipecotic acid were similar to those of NO711 and SNAP-5114 together. We conclude that synaptic GABA levels in neocortical neurons are controlled primarily by GAT-1, but that GAT-1 and GAT-2/3 work together extrasynaptically to limit tonic currents. Inhibition of any one GAT subtype does not increase the tonic current, presumably as a result of increased activity of the remaining transporters. Thus neocortical GAT-1 and GAT-2/3 have distinct but overlapping roles in modulating GABA conductances.
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Affiliation(s)
- Sotirios Keros
- Department of Neurobiology and Civitan International Research Center, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
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47
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Ren Q, Paulsen IT. Comparative analyses of fundamental differences in membrane transport capabilities in prokaryotes and eukaryotes. PLoS Comput Biol 2005; 1:e27. [PMID: 16118665 PMCID: PMC1188273 DOI: 10.1371/journal.pcbi.0010027] [Citation(s) in RCA: 123] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2005] [Accepted: 07/08/2005] [Indexed: 11/19/2022] Open
Abstract
Whole-genome transporter analyses have been conducted on 141 organisms whose complete genome sequences are available. For each organism, the complete set of membrane transport systems was identified with predicted functions, and classified into protein families based on the transporter classification system. Organisms with larger genome sizes generally possessed a relatively greater number of transport systems. In prokaryotes and unicellular eukaryotes, the significant factor in the increase in transporter content with genome size was a greater diversity of transporter types. In contrast, in multicellular eukaryotes, greater number of paralogs in specific transporter families was the more important factor in the increase in transporter content with genome size. Both eukaryotic and prokaryotic intracellular pathogens and endosymbionts exhibited markedly limited transport capabilities. Hierarchical clustering of phylogenetic profiles of transporter families, derived from the presence or absence of a certain transporter family, showed that clustering patterns of organisms were correlated to both their evolutionary history and their overall physiology and lifestyles. Membrane transporters are the cell's equivalent of delivery vehicles, garbage disposals, and communication systems—proteins that negotiate through cell membranes to deliver essential nutrients, eject waste products, and help the cell sense environmental conditions around it. Membrane transport systems play crucial roles in fundamental cellular processes of all organisms. The suite of transporters in any one organism also sheds light on its lifestyle and physiology. Up to now, analysis of membrane transporters has been limited mainly to the examination of transporter genes of individual organisms. But advances in genome sequencing have now made it possible for scientists to compare transport and other essential cellular processes across a range of organisms in all three domains of life. Ren and Paulsen present the first comprehensive bioinformatic analysis of the predicted membrane transporter content of 141 different prokaryotic and eukaryotic organisms. The scientists developed a new computational application of the phylogenetic profiling approach to cluster together organisms that appear to have similar suites of transporters. For example, a group of obligate intracellular pathogens and endosymbionts possess only limited transporter systems in spite of the massive metabolite fluxes one would expect between the symbionts and their host. This is likely due to the relatively static nature of their intracellular environment. In contrast, a cluster of plant/soil-associated microbes encode a robust array of transporters, reflecting the organisms' versatility as well as their exposure to a wide range of different substrates in their natural environment.
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Affiliation(s)
- Qinghu Ren
- The Institute for Genomic Research, Rockville, Maryland, United States of America
| | - Ian T Paulsen
- The Institute for Genomic Research, Rockville, Maryland, United States of America
- * To whom correspondence should be addressed. E-mail:
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48
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Galvan A, Villalba RM, West SM, Maidment NT, Ackerson LC, Smith Y, Wichmann T. GABAergic Modulation of the Activity of Globus Pallidus Neurons in Primates: In Vivo Analysis of the Functions of GABA Receptors and GABA Transporters. J Neurophysiol 2005; 94:990-1000. [PMID: 15829599 DOI: 10.1152/jn.00068.2005] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Neurons in the external and internal segment of the globus pallidus (GPe and GPi, respectively) receive substantial GABAergic inputs from the striatum and through axon collaterals of neighboring pallidal neurons. The effects of GABA on pallidal activity depend on the synaptic localization of GABA receptors and the distribution and activity of GABA transporters (GATs). To explore the contribution of GABA receptors and transporters to pallidal function, we recorded the activity of single neurons in GPe or GPi before, during, and after local microinjections of GABAergic compounds in awake rhesus monkeys. Activation of GABAA or GABAB receptors with muscimol or baclofen, respectively, inhibited pallidal activity. These effects were reversed by concomitant infusion of the respective GABA receptor antagonists, gabazine and CGP-55845. Given alone, the antagonists were without consistent effect. Application of the selective GAT-1 inhibitor, SKF-89976A, and the semiselective GAT-3 blocker, SNAP-5114, decreased pallidal activity. Both GAT inhibitors increased GABA levels in the pallidum, as measured by microdialysis. Electron microscopic observations revealed that these transporters are located on glial processes and unmyelinated axonal segments, but rarely on terminals. Our results indicate that activation of GABAA and GABAB receptors inhibits neuronal activity in both segments of the pallidum. GAT-1 and GAT-3 are involved in the modulation of endogenous GABA levels and may be important in regulating the extrasynaptic levels of GABA. Together with previous evidence that a considerable proportion of pallidal GABA receptors are located outside the synaptic cleft, our experiments strongly support the importance of extrasynaptic GABAergic transmission in the primate pallidum.
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Affiliation(s)
- Adriana Galvan
- Department of Neurology, Emory University, Atlanta, GA 30322, USA.
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49
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Raol YH, Zhang G, Budreck EC, Brooks-Kayal AR. Long-term effects of diazepam and phenobarbital treatment during development on GABA receptors, transporters and glutamic acid decarboxylase. Neuroscience 2005; 132:399-407. [PMID: 15802192 DOI: 10.1016/j.neuroscience.2005.01.005] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/09/2005] [Indexed: 11/26/2022]
Abstract
Diazepam (DZ) and phenobarbital (PH) are commonly used to treat early-life seizures and act on GABAA receptors (GABAR). The developing GABAergic system is highly plastic, and the long-term effects of postnatal treatment with these drugs on the GABAergic system has not been extensively examined. In the present study, we investigated the effects of prolonged DZ and PH treatment during postnatal development and then discontinuation on expression of a variety of genes involved in GABAergic neurotransmission during adulthood. Rat pups were treated with DZ, PH or vehicle from postnatal day (P) 10-P40 and then the dose was tapered for 2 weeks and terminated at P55. Expression of GABAR subunits, GABAB receptor subunits, GABA transporters (GAT) and GABA synthesizing enzymes (glutamic acid decarboxylase: GAD) mRNAs in hippocampal dentate granule neurons (DGNs) were analyzed using antisense RNA amplification at P90. Protein levels for the alpha1 subunit of GABAR, GAD67, GAT1 and 3 were also assessed using Western blotting. At P90, mRNA expression for GAT-1, 3, 4, GABAR subunits alpha4, alpha6, beta3, delta and theta and GABAB receptor subunit R1 was increased and mRNA expression for GAD65, GAD67 and GABAR subunits alpha1 and alpha3 were decreased in DGNs of rats treated with DZ and PH. The current data suggest that prolonged DZ and PH treatment during postnatal development causes permanent alterations in the expression of hippocampal GABA receptor subunits, GATs and GAD long after therapy has ended.
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Affiliation(s)
- Y H Raol
- Division of Neurology, Pediatric Regional Epilepsy Program, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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50
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Abstract
OBJECTIVE To review the recent advances in knowledge about human transporters and their effect on drug disposition. DATA SOURCES A MEDLINE search (1996-March 2005) was performed to identify pertinent literature on human transporters and their impact on drug disposition. Additional articles were identified from a manual search of the references of retrieved articles. STUDY SELECTION AND DATA EXTRACTION Based on the identified studies, data were extracted on the impact of transporters on drug absorption, distribution, and elimination. DATA SYNTHESIS The pharmacokinetic disposition of drugs is known to be influenced by metabolic enzymes, kidney function, and transporters. Recent research on human transporters has greatly advanced our understanding of their diversity and importance in drug disposition. In particular, members of the multidrug resistance family of transporters (MDR, MRP) are present in organs and tissues throughout the body and are known to significantly affect the absorption, distribution, and elimination of commonly prescribed drugs. A growing number of studies now demonstrate that alterations in transporter function as a result of drug interactions or genetic polymorphisms may explain a significant portion of the variability in treatment response for certain drugs. CONCLUSIONS Human transporters contribute significantly to the pharmacokinetic disposition of drugs. Knowledge of substrates, inducers, and inhibitors of these transporters is necessary to ensure optimal patient outcomes.
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Affiliation(s)
- Paul M Beringer
- Department of Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90089-9121, USA.
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