1
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Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. Nat Commun 2024; 15:3574. [PMID: 38678027 PMCID: PMC11055893 DOI: 10.1038/s41467-024-48030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/17/2024] [Indexed: 04/29/2024] Open
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that other CDO-like enzymes are likely enzyme filaments. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
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Affiliation(s)
- Michael P Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA
| | - Tobias W Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, 48109, USA.
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2
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Wei H, Wang B, Xu Y, Fan W, Zhang M, Huang F, Shi C, Li T, Wang S, Wang S. The Mechanism of Ovule Abortion in Self-Pollinated 'Hanfu' Apple Fruits and Related Gene Screening. PLANTS (BASEL, SWITZERLAND) 2024; 13:996. [PMID: 38611525 PMCID: PMC11013273 DOI: 10.3390/plants13070996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024]
Abstract
Apples exhibit S-RNase-mediated self-incompatibility and typically require cross-pollination in nature. 'Hanfu' is a cultivar that produces abundant fruit after self-pollination, although it also shows a high rate of seed abortion afterwards, which greatly reduces fruit quality. In this study, we investigated the ovule development process and the mechanism of ovule abortion in apples after self-pollination. Using a DIC microscope and biomicroscope, we found that the abortion of apple ovules occurs before embryo formation and results from the failure of sperm-egg fusion. Further, we used laser-assisted microdissection (LAM) cutting and sperm and egg cell sequencing at different periods after pollination to obtain the genes related to ovule abortion. The top 40 differentially expressed genes (DEGs) were further verified, and the results were consistent with switching the mechanism at the 5' end of the RNA transcript (SMART-seq). Through this study, we can preliminarily clarify the mechanism of ovule abortion in self-pollinated apple fruits and provide a gene reserve for further study and improvement of 'Hanfu' apple fruit quality.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shengnan Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
| | - Shengyuan Wang
- College of Horticulture, China Agricultural University, Beijing 100193, China
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3
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Berg HY, Arju G, Becerra-Rodríguez C, Galeote V, Nisamedtinov I. Unlocking the secrets of peptide transport in wine yeast: insights into oligopeptide transporter functions and nitrogen source preferences. Appl Environ Microbiol 2023; 89:e0114123. [PMID: 37843270 PMCID: PMC10686055 DOI: 10.1128/aem.01141-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/27/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Limited nitrogen supply can prevent the completion of alcoholic fermentation. Supplementation through peptides as an alternative, natural source of nitrogen for yeast offers an interesting solution for this issue. In this work, the S. cerevisiae peptide transporters of the Opt and Fot families were studied. We demonstrated that Fot and Opt2 have a broader peptide length preference than previously reported, enabling yeasts to acquire sufficient nitrogen from peptides without requiring additional ammonia or amino acids to complete fermentation. On the contrary, Opt1 was unable to consume any peptide in the given conditions, whereas it has been described elsewhere as the main peptide transporter for peptides longer than three amino acid residues in experiments in laboratory conditions. This controversy signifies the need in applied sciences for approaching experimental conditions to those prevalent in the industry for its more accurate characterization. Altogether, this work provides further evidence of the importance of peptides as a nitrogen source for yeast and their consequent positive impact on fermentation kinetics.
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Affiliation(s)
- Hidde Yaël Berg
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
- Center of Food and Fermentation Technologies, Tallinn, Estonia
| | - Georg Arju
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | | | - Virginie Galeote
- SPO, Univ. Montpellier, INRAE, Institut Agro, Montpellier, France
| | - Ildar Nisamedtinov
- Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
- Lallemand, Inc., Montreal, Canada
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4
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Andreas MP, Giessen TW. Cyclodipeptide oxidase is an enzyme filament. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559410. [PMID: 37808672 PMCID: PMC10557607 DOI: 10.1101/2023.09.25.559410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Modified cyclic dipeptides represent a widespread class of secondary metabolites with diverse pharmacological activities, including antibacterial, antifungal, and antitumor. Here, we report the structural characterization of the Streptomyces noursei enzyme AlbAB, a cyclodipeptide oxidase (CDO) carrying out α,β-dehydrogenations during the biosynthesis of the antibiotic albonoursin. We show that AlbAB is a megadalton heterooligomeric enzyme filament containing covalently bound flavin mononucleotide cofactors. We highlight that AlbAB filaments consist of alternating dimers of AlbA and AlbB and that enzyme activity is crucially dependent on filament formation. We show that AlbA-AlbB interactions are highly conserved suggesting that all CDO-like enzymes are likely enzyme filaments. Our work represents the first structural characterization of a CDO. As CDOs have been employed in the structural diversification of cyclic dipeptides, our results will be useful for future applications of CDOs in biocatalysis and chemoenzymatic synthesis.
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Affiliation(s)
- Michael P. Andreas
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Tobias W. Giessen
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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5
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Wu J, Li R, Shen Y, Zhang X, Wang X, Wang Z, Zhao Y, Huang L, Zhang L, Zhang B. Candida tropicalis oligopeptide transporters assist in the transmembrane transport of the antimicrobial peptide CGA-N9. Biochem Biophys Res Commun 2023; 649:101-109. [PMID: 36764112 DOI: 10.1016/j.bbrc.2023.01.083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 01/26/2023] [Indexed: 02/05/2023]
Abstract
Candida tropicalis is often reported as the second or third most common pathogen causing fungal infections. Antimicrobial peptides (AMPs) have attracted increasing attention for their broad-spectrum antimicrobial properties and low cytotoxicity. Our previous studies have shown that CGA-N9, a non-membrane-rupturing AMP, crosses the cell membrane to exert anticandidal activity. We speculate that there are some related transporters that assist in the transmembrane transport of CGA-N9. In this study, the relationship between CGA-N9 lethality kinetics and its real-time transmembrane amount in C. tropicalis cells was investigated. The results demonstrated that there was a positive correlation between its candicidal activity and transmembrane amount. A total of 12 oligopeptide transporter (OPT) coding sequences (CDSs) were cloned from C. tropicalis by using the conservative OPT gene sequences of Candida spp. to design primers and were named C. tropicalis OPTs (CtOPTs). The results of RT‒qPCR demonstrated that the expression levels of CtOPT1, CtOPT9 and CtOPT12 were correlated with the CGA-N9 transmembrane amount in a time-dependent manner. The results of molecular docking demonstrated that CtOPT1, CtOPT9 and CtOPT12 interact strongly with CGA-N9. Therefore, CtOPT1, CtOPT9 and CtOPT12 were predicted to assist in the transmembrane transport of the AMP CGA-N9.
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Affiliation(s)
- Jiasha Wu
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Ruifang Li
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China.
| | - Yunpeng Shen
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Xinhui Zhang
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Xueqin Wang
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Zichao Wang
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Yingyuan Zhao
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Liang Huang
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Lan Zhang
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China
| | - Beibei Zhang
- College of Biological Engineering, Henan University of Technology, 450001, Zhengzhou, Henan, PR China; Key Laboratory of Functional Molecules for Biomedical Research, Henan University of Technology, 450001, Zhengzhou, Henan, PR China.
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6
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Methodology for Analysis of Peptide Consumption by Yeast during Fermentation of Enzymatic Protein Hydrolysate Supplemented Synthetic Medium Using UPLC-IMS-HRMS. FERMENTATION 2022. [DOI: 10.3390/fermentation8040145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Several studies have shown the ability of yeast to consume peptides as a nitrogen source in single-peptide containing media. However, a suitable and cost-effective methodology to study the utilization of peptides by yeast and other microorganisms in a complex peptide mixture has yet to be put forward. This article addresses this issue by presenting a screening methodology for tracking the consumption of peptides by yeast during alcoholic fermentation. As a peptide source, the methodology makes use of an in-house prepared peptide-mapped bovine serum albumin (BSA) proteolytic digest, which was applied to a synthetic grape must. The peptide uptake was analyzed using high-throughput ultra-high-pressure liquid chromatography coupled to data-independent acquisition-based ion mobility separation-enabled high-resolution mass spectrometry (UPLC-DIA-IMS-HRMS) analysis. The relative changes of abundance of 123 di- to hexapeptides were monitored and reported during fermentations with three commercial wine strains, demonstrating different uptake kinetics for individual peptides. Using the same peptide-mapped BSA hydrolysate, the applicability of an untargeted workflow was additionally assessed for peptide profiling in unelucidated matrixes. The comparison of the results from peptide mapping and untargeted analysis experiments highlighted the ability of untargeted analysis to consistently identify small molecular weight peptides on the length and amino acid composition. The proposed method, in combination with other analytical techniques, such as gene or protein expression analysis, can be a useful tool for different metabolic studies related to the consumption of complex nitrogen sources by yeast or other microorganisms.
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7
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Metalloprotein-Specific or Critical Amino Acid Residues: Perspectives on Plant-Precise Detoxification and Recognition Mechanisms under Cadmium Stress. Int J Mol Sci 2022; 23:ijms23031734. [PMID: 35163656 PMCID: PMC8836122 DOI: 10.3390/ijms23031734] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/26/2022] [Accepted: 02/02/2022] [Indexed: 12/15/2022] Open
Abstract
Cadmium (Cd) pollution in cultivated land is caused by irresistible geological factors and human activities; intense diffusion and migration have seriously affected the safety of food crops. Plants have evolved mechanisms to control excessive influx of Cd in the environment, such as directional transport, chelation and detoxification. This is done by some specific metalloproteins, whose key amino acid motifs have been investigated by scientists one by one. The application of powerful cell biology, crystal structure science, and molecular probe targeted labeling technology has identified a series of protein families involved in the influx, transport and detoxification of the heavy metal Cd. This review summarizes them as influx proteins (NRAMP, ZIP), chelating proteins (MT, PDF), vacuolar proteins (CAX, ABCC, MTP), long-distance transport proteins (OPT, HMA) and efflux proteins (PCR, ABCG). We selected representative proteins from each family, and compared their amino acid sequence, motif structure, subcellular location, tissue specific distribution and other characteristics of differences and common points, so as to summarize the key residues of the Cd binding target. Then, we explain its special mechanism of action from the molecular structure. In conclusion, this review is expected to provide a reference for the exploration of key amino acid targets of Cd, and lay a foundation for the intelligent design and breeding of crops with high/low Cd accumulation.
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Wang Y, Zhang X, Luo B, Hu H, Zhong H, Zhang H, Zhang Z, Gao J, Liu D, Wu L, Gao S, Gao D, Gao S. Identification of a new mutant allele of ZmYSL2 that regulates kernel development and nutritional quality in maize. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:7. [PMID: 37309320 PMCID: PMC10248714 DOI: 10.1007/s11032-022-01278-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/20/2022] [Indexed: 06/14/2023]
Abstract
The discovery and characterization of the opaque endosperm gene provide ideas and resources for the production and application of maize. We found an o213 mutant whose phenotype was opaque and shrunken endosperm with semi-dwarf plant height. The protein, lipid, and starch contents in the o213 endosperm were significantly decreased, while the free amino acid content in the o213 endosperm significantly increased. The aspartic acid, asparagine, and lysine contents were raised in the o213 endosperm by 6.5-, 8.5-, and 1.7-fold, respectively. Genetic analysis showed that this o213 mutant is a recessive single-gene mutation. The position mapping indicated that o213 is located in a 468-kb region that contains 11 protein-encoding genes on the long arm of chromosome 5. The coding sequence analysis of candidate genes between the WT and o213 showed that ZmYSL2 had only a single-base substitution (A-G) in the fifth exon, which caused methionine substitution to valine. Sequence analysis and the allelic test showed that o213 is a new mutant allele of ZmYSL2. The qRT-PCR results indicated that o213 is highly expressed in the stalks and anthers. Subcellular localization studies showed that o213 is a membrane transporter. In the variation analysis of o213, the amplification of 65 inbred lines in GWAS showed that this 3-bp deletion of the first exon of o213 was found only in temperate inbred lines, implying that the gene was artificially affected in the selection process. Our results suggest that o213 is an important endosperm development gene and may serve as a genetic resource. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01278-9.
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Affiliation(s)
- Yikai Wang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Xiao Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Bowen Luo
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Hongmei Hu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Haixu Zhong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Haiying Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Zhicheng Zhang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Jiajia Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Dan Liu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Ling Wu
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Shiqiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Duojiang Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
| | - Shibin Gao
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130 Sichuan China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Chengdu, 611130 Sichuan China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, 611130 Sichuan China
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9
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Becerra-Rodríguez C, Marsit S, Galeote V. Diversity of Oligopeptide Transport in Yeast and Its Impact on Adaptation to Winemaking Conditions. Front Genet 2020; 11:602. [PMID: 32587604 PMCID: PMC7298112 DOI: 10.3389/fgene.2020.00602] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Nitrogen is an essential nutrient for yeasts and its relative abundance is an important modulator of fermentation kinetics. The main sources of nitrogen in food are ammonium and free amino acids, however, secondary sources such as oligopeptides are also important contributors to the nitrogen supply. In yeast, oligopeptide uptake is driven by different families of proton–coupled transporters whose specificity depends on peptide length. Proton-dependent Oligopeptide Transporters (POT) are specific to di- and tri-peptides, whereas the Oligopeptide Transport (OPT) family members import tetra- and pentapeptides. Recently, the novel family of Fungal Oligopeptide Transporters (FOT) has been identified in Saccharomyces cerevisiae wine strains as a result of a horizontal gene transfer from Torulaspora microellipsoides. In natural grape must fermentations with S. cerevisiae, Fots have a broader range of oligopeptide utilization in comparison with non-Fot strains, leading to higher biomass production and better fermentation efficiency. In this review we present the current knowledge on the diversity of oligopeptide transporters in yeast, also discussing how the consumption of oligopeptides provides an adaptive advantage to yeasts within the wine environment.
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Affiliation(s)
| | - Souhir Marsit
- Institut de Biologie Intégrative et des Systèmes, Regroupement Québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines, (PROTEO), Département de Biologie, Université Laval, Québec City, QC, Canada
| | - Virginie Galeote
- SPO, INRAE, Université de Montpellier, Montpellier SupAgro, Montpellier, France
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10
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Xie XL, Wei Y, Song YY, Pan GM, Chen LN, Wang G, Zhang SH. Genetic Analysis of Four Sexual Differentiation Process Proteins (isp4/SDPs) in Chaetomium thermophilum and Thermomyces lanuginosus Reveals Their Distinct Roles in Development. Front Microbiol 2020; 10:2994. [PMID: 31969873 PMCID: PMC6956688 DOI: 10.3389/fmicb.2019.02994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/10/2019] [Indexed: 12/29/2022] Open
Abstract
Fungal sexual development requires the involvement of a large number of functional genes. Fungal genes encoding sexual differentiation process proteins (SDPs), isps, have been known for decades. isp4/SDP and its homologs function as oligopeptide transporters (OPTs), yet their roles in reproduction are unknown. Here, we genetically analyzed all four isp4/SDP homologs in the sexual species Chaetomium thermophilum and asexual species Thermomyces lanuginosus. Using single gene deletion mutants, we found that T. lanuginosus SDP (TlSDP) participated in asexual sporulation, whereas the other homologs participated in sexual morphogenesis. In complementary tests, C. thermophilum SDPs (CtSDP1-3) restored sporulation defects in TlSDP deletion strains (ΔTlSDP), and their translated proteins, which were localized onto the cytomembrane, possessed OPT activity. Interestingly, CtSDP2 accumulated at the top of the hyphae played a distinct role in determining the sexual cycle, glutathione transport, and lifespan shortening. A unique 72nt-insertion fragment (72INS) was discovered in CtSDP2. Biological analysis of the 72INS deletion and DsRED-tagged fusion strains implied the involvement of 72INS in fungal growth and development. In contrast to TlSDP, which only contributes to conidial production, the three CtSDPs play important roles in sexual and asexual reproduction, and CtSDP2 harbors a unique functional 72INS that initiates sexual morphogenesis.
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Affiliation(s)
- Xiang-Li Xie
- College of Plant Sciences, Jilin University, Changchun, China
| | - Yi Wei
- College of Plant Sciences, Jilin University, Changchun, China
| | - Yan-Yue Song
- College of Plant Sciences, Jilin University, Changchun, China
| | - Guan-Ming Pan
- College of Plant Sciences, Jilin University, Changchun, China
| | - Li-Na Chen
- College of Plant Sciences, Jilin University, Changchun, China
| | - Gang Wang
- School of Life Sciences, Henan University, Kaifeng, China
| | - Shi-Hong Zhang
- College of Plant Sciences, Jilin University, Changchun, China
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11
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Genome-Wide Identification and Comparative Analysis for OPT Family Genes in Panax ginseng and Eleven Flowering Plants. Molecules 2018; 24:molecules24010015. [PMID: 30577553 PMCID: PMC6337337 DOI: 10.3390/molecules24010015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/06/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023] Open
Abstract
Herb genomics and comparative genomics provide a global platform to explore the genetics and biology of herbs at the genome level. Panax ginseng C.A. Meyer is an important medicinal plant for a variety of bioactive chemical compounds of which the biosynthesis may involve transport of a wide range of substrates mediated by oligopeptide transporters (OPT). However, information about the OPT family in the plant kingdom is still limited. Only 17 and 18 OPT genes have been characterized for Oryza sativa and Arabidopsisthaliana, respectively. Additionally, few comprehensive studies incorporating the phylogeny, gene structure, paralogs evolution, expression profiling, and co-expression network between transcription factors and OPT genes have been reported for ginseng and other species. In the present study, we performed those analyses comprehensively with both online tools and standalone tools. As a result, we identified a total of 268 non-redundant OPT genes from 12 flowering plants of which 37 were from ginseng. These OPT genes were clustered into two distinct clades in which clade-specific motif compositions were considerably conservative. The distribution of OPT paralogs was indicative of segmental duplication and subsequent structural variation. Expression patterns based on two sources of RNA-Sequence datasets suggested that some OPT genes were expressed in both an organ-specific and tissue-specific manner and might be involved in the functional development of plants. Further co-expression analysis of OPT genes and transcription factors indicated 141 positive and 11 negative links, which shows potent regulators for OPT genes. Overall, the data obtained from our study contribute to a better understanding of the complexity of the OPT gene family in ginseng and other flowering plants. This genetic resource will help improve the interpretation on mechanisms of metabolism transportation and signal transduction during plant development for Panax ginseng.
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12
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Xiang Q, Shen K, Yu X, Zhao K, Gu Y, Zhang X, Chen X, Chen Q. Analysis of the oligopeptide transporter gene family in Ganoderma lucidum: structure, phylogeny, and expression patterns. Genome 2017; 60:293-302. [DOI: 10.1139/gen-2016-0120] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Oligopeptide transporters (OPTs) are believed to transport broad ranges of substrates across the plasma membrane from the extracellular environment into the cell and are thought to contribute to various biological processes. In the present study, 13 putative OPTs (Gl-OPT1 to Gl-OPT13) were identified through extensive search of Ganoderma lucidum genome database. Phylogenetic analysis with OPTs from other fungi and plants indicates that these genes can be further divided into five groups. Motif compositions of OPT members are highly conserved in each group, indicative of functional conservation. Expression profile analysis of the 13 Gl-OPT genes indicated that, with the exception of Gl-OPT7–Gl-OPT9, for which no transcripts were detected, all paralogues were differentially expressed, suggesting their potential involvement in stress response and functional development of fungi. Overall, the analyses in this study provide a starting point for elucidating the functions of OPT in G. lucidum, and for understanding the complexities of metabolic regulation.
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Affiliation(s)
- Quanju Xiang
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Keyu Shen
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiumei Yu
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Ke Zhao
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Yunfu Gu
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaoping Zhang
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Xiaoqiong Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Qiang Chen
- College of Resource, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
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Bisson MMA, Kessenbrock M, Müller L, Hofmann A, Schmitz F, Cristescu SM, Groth G. Peptides interfering with protein-protein interactions in the ethylene signaling pathway delay tomato fruit ripening. Sci Rep 2016; 6:30634. [PMID: 27477591 PMCID: PMC4967898 DOI: 10.1038/srep30634] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2015] [Accepted: 07/07/2016] [Indexed: 01/18/2023] Open
Abstract
The plant hormone ethylene is involved in the regulation of several processes with high importance for agricultural applications, e.g. ripening, aging and senescence. Previous work in our group has identified a small peptide (NOP-1) derived from the nuclear localization signal of the Arabidopsis ethylene regulator ETHYLENE INSENSITIVE-2 (EIN2) C-terminal part as efficient inhibitor of ethylene responses. Here, we show that NOP-1 is also able to efficiently disrupt EIN2-ETR1 complex formation in tomato, indicating that the NOP-1 inhibition mode is conserved across plant species. Surface application of NOP-1 on green tomato fruits delays ripening similar to known inhibitors of ethylene perception (MCP) and ethylene biosynthesis (AVG). Fruits treated with NOP-1 showed similar ethylene production as untreated controls underlining that NOP-1 blocks ethylene signaling by targeting an essential interaction in this pathway, while having no effect on ethylene biosynthesis.
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Affiliation(s)
- Melanie M. A. Bisson
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Mareike Kessenbrock
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Lena Müller
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Alexander Hofmann
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Florian Schmitz
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
| | - Simona M. Cristescu
- Department of Molecular and Laser Physics, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Georg Groth
- Biochemical Plant Physiology, Heinrich-Heine-University Düsseldorf, D-40204 Düsseldorf, Germany
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14
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Thakur A, Bachhawat AK. Charged/Polar-residue scanning of the hydrophobic face of transmembrane domain 9 of the yeast glutathione transporter, hgt1p, reveals a conformationally critical region for substrate transport. G3 (BETHESDA, MD.) 2015; 5:921-9. [PMID: 25784163 PMCID: PMC4426376 DOI: 10.1534/g3.115.017079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/12/2015] [Indexed: 11/18/2022]
Abstract
Unraveling the mechanistic workings of membrane transporters has remained a challenging task. We describe a novel strategy that involves subjecting the residues of the hydrophobic face of a transmembrane helix to a charged/polar scanning mutagenesis. TMD9 of the yeast glutathione transporter, Hgt1p, has been identified as being important in substrate binding, and two residues, F523 and Q526, are expected to line the substrate translocation channel while the other face is hydrophobic. The hydrophobic face of TMD9 helix consists of residues A509, V513, L517, L520, I524, and I528, and these were mutated to lysine, glutamine, and glutamic acid. Among the 16 charged mutants created, six were nonfunctional, revealing a surprising tolerance of charged residues in the hydrophobic part of TM helices. Furthermore, the only position that did not tolerate any charged residue was I524, proximal to the substrate binding residues. However, P525, also proximal to the substrate binding residues, did tolerate charged/polar residues, suggesting that mere proximity to the substrate binding residues was not the only factor. The I524K/E/Q mutants expressed well and localized correctly despite lacking any glutathione uptake capability. Isolation of suppressors for all nonfunctional mutants yielded second-site suppressors only for I524K and I524Q, and suppressors for these mutations appeared at G202K/I and G202K/Q, respectively. G202 is in the hydrophilic loop between TMD3 and TMD4. The results suggest that I524 in the hydrophobic face interacts with this region and is also in a conformationally critical region for substrate translocation.
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Affiliation(s)
- Anil Thakur
- Institute of Microbial Technology (IMTECH), Sector 39-A Chandigarh 160036, India Indian Institute of Science Education & Research (IISER) Mohali, Knowledge City, S.A.S. Nagar, Punjab 140306, India
| | - Anand K Bachhawat
- Institute of Microbial Technology (IMTECH), Sector 39-A Chandigarh 160036, India
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15
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Ramakrishnan G, Ochoa-Montaño B, Raghavender US, Mudgal R, Joshi AG, Chandra NR, Sowdhamini R, Blundell TL, Srinivasan N. Enriching the annotation of Mycobacterium tuberculosis H37Rv proteome using remote homology detection approaches: insights into structure and function. Tuberculosis (Edinb) 2014; 95:14-25. [PMID: 25467293 DOI: 10.1016/j.tube.2014.10.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 10/14/2014] [Accepted: 10/27/2014] [Indexed: 12/01/2022]
Abstract
The availability of the genome sequence of Mycobacterium tuberculosis H37Rv has encouraged determination of large numbers of protein structures and detailed definition of the biological information encoded therein; yet, the functions of many proteins in M. tuberculosis remain unknown. The emergence of multidrug resistant strains makes it a priority to exploit recent advances in homology recognition and structure prediction to re-analyse its gene products. Here we report the structural and functional characterization of gene products encoded in the M. tuberculosis genome, with the help of sensitive profile-based remote homology search and fold recognition algorithms resulting in an enhanced annotation of the proteome where 95% of the M. tuberculosis proteins were identified wholly or partly with information on structure or function. New information includes association of 244 proteins with 205 domain families and a separate set of new association of folds to 64 proteins. Extending structural information across uncharacterized protein families represented in the M. tuberculosis proteome, by determining superfamily relationships between families of known and unknown structures, has contributed to an enhancement in the knowledge of structural content. In retrospect, such superfamily relationships have facilitated recognition of probable structure and/or function for several uncharacterized protein families, eventually aiding recognition of probable functions for homologous proteins corresponding to such families. Gene products unique to mycobacteria for which no functions could be identified are 183. Of these 18 were determined to be M. tuberculosis specific. Such pathogen-specific proteins are speculated to harbour virulence factors required for pathogenesis. A re-annotated proteome of M. tuberculosis, with greater completeness of annotated proteins and domain assigned regions, provides a valuable basis for experimental endeavours designed to obtain a better understanding of pathogenesis and to accelerate the process of drug target discovery.
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Affiliation(s)
- Gayatri Ramakrishnan
- Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India; Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | | | - Upadhyayula S Raghavender
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vignyan Kendra Campus, Bangalore 560065, India.
| | - Richa Mudgal
- Indian Institute of Science Mathematics Initiative, Indian Institute of Science, Bangalore 560012, India; Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.
| | - Adwait G Joshi
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vignyan Kendra Campus, Bangalore 560065, India; Manipal University, Manipal, Karnataka 576104, India.
| | - Nagasuma R Chandra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
| | - Ramanathan Sowdhamini
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Gandhi Krishi Vignyan Kendra Campus, Bangalore 560065, India.
| | - Tom L Blundell
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.
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16
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Elbaz-Alon Y, Morgan B, Clancy A, Amoako TNE, Zalckvar E, Dick TP, Schwappach B, Schuldiner M. The yeast oligopeptide transporter Opt2 is localized to peroxisomes and affects glutathione redox homeostasis. FEMS Yeast Res 2014; 14:1055-67. [PMID: 25130273 DOI: 10.1111/1567-1364.12196] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 07/08/2014] [Accepted: 08/07/2014] [Indexed: 11/28/2022] Open
Abstract
Glutathione, the most abundant small-molecule thiol in eukaryotic cells, is synthesized de novo solely in the cytosol and must subsequently be transported to other cellular compartments. The mechanisms of glutathione transport into and out of organelles remain largely unclear. We show that budding yeast Opt2, a close homolog of the plasma membrane glutathione transporter Opt1, localizes to peroxisomes. We demonstrate that deletion of OPT2 leads to major defects in maintaining peroxisomal, mitochondrial, and cytosolic glutathione redox homeostasis. Furthermore, ∆opt2 strains display synthetic lethality with deletions of genes central to iron homeostasis that require mitochondrial glutathione redox homeostasis. Our results shed new light on the importance of peroxisomes in cellular glutathione homeostasis.
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Affiliation(s)
- Yael Elbaz-Alon
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Holland LM, Schröder MS, Turner SA, Taff H, Andes D, Grózer Z, Gácser A, Ames L, Haynes K, Higgins DG, Butler G. Comparative phenotypic analysis of the major fungal pathogens Candida parapsilosis and Candida albicans. PLoS Pathog 2014; 10:e1004365. [PMID: 25233198 PMCID: PMC4169492 DOI: 10.1371/journal.ppat.1004365] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 07/28/2014] [Indexed: 01/15/2023] Open
Abstract
Candida parapsilosis and Candida albicans are human fungal pathogens that belong to the CTG clade in the Saccharomycotina. In contrast to C. albicans, relatively little is known about the virulence properties of C. parapsilosis, a pathogen particularly associated with infections of premature neonates. We describe here the construction of C. parapsilosis strains carrying double allele deletions of 100 transcription factors, protein kinases and species-specific genes. Two independent deletions were constructed for each target gene. Growth in >40 conditions was tested, including carbon source, temperature, and the presence of antifungal drugs. The phenotypes were compared to C. albicans strains with deletions of orthologous transcription factors. We found that many phenotypes are shared between the two species, such as the role of Upc2 as a regulator of azole resistance, and of CAP1 in the oxidative stress response. Others are unique to one species. For example, Cph2 plays a role in the hypoxic response in C. parapsilosis but not in C. albicans. We found extensive divergence between the biofilm regulators of the two species. We identified seven transcription factors and one protein kinase that are required for biofilm development in C. parapsilosis. Only three (Efg1, Bcr1 and Ace2) have similar effects on C. albicans biofilms, whereas Cph2, Czf1, Gzf3 and Ume6 have major roles in C. parapsilosis only. Two transcription factors (Brg1 and Tec1) with well-characterized roles in biofilm formation in C. albicans do not have the same function in C. parapsilosis. We also compared the transcription profile of C. parapsilosis and C. albicans biofilms. Our analysis suggests the processes shared between the two species are predominantly metabolic, and that Cph2 and Bcr1 are major biofilm regulators in C. parapsilosis. Candida species are among the most common causes of fungal infection worldwide. Infections can be both community-based and hospital-acquired, and are particularly associated with immunocompromised individuals. Candida albicans is the most commonly isolated species and is the best studied. However, other species are becoming of increasing concern. Candida parapsilosis causes outbreaks of infection in neonatal wards, and is one of the few Candida species that is transferred from the hands of healthcare workers. C. parapsilosis, like C. albicans, grows as biofilms (cell communities) on the surfaces of indwelling medical devices like feeding tubes. We describe here the construction of a set of tools that allow us to characterize the virulence properties of C. parapsilosis, and in particular its ability to grow as biofilms. We find that some of the regulatory mechanisms are shared with C. albicans, but others are unique to each species. Our tools, based on selectively deleting regulatory genes, will provide a major resource to the fungal research community.
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Affiliation(s)
- Linda M. Holland
- School of Biomedical and Biomolecular Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Markus S. Schröder
- School of Biomedical and Biomolecular Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Siobhán A. Turner
- School of Biomedical and Biomolecular Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Heather Taff
- Departments of Medicine and Microbiology and Immunology, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - David Andes
- Departments of Medicine and Microbiology and Immunology, University of Wisconsin, Madison, Madison, Wisconsin, United States of America
| | - Zsuzsanna Grózer
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Attila Gácser
- Department of Microbiology, University of Szeged, Szeged, Hungary
| | - Lauren Ames
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Ken Haynes
- School of Biosciences, University of Exeter, Exeter, Devon, United Kingdom
| | - Desmond G. Higgins
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Geraldine Butler
- School of Biomedical and Biomolecular Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
- * E-mail:
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Grillet L, Mari S, Schmidt W. Iron in seeds - loading pathways and subcellular localization. FRONTIERS IN PLANT SCIENCE 2014; 4:535. [PMID: 24427161 PMCID: PMC3877777 DOI: 10.3389/fpls.2013.00535] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/11/2013] [Indexed: 05/04/2023]
Abstract
Iron (Fe) is one of the most abundant elements on earth, but its limited bioavailability poses a major constraint for agriculture and constitutes a serious problem in human health. Due to an improved understanding of the mechanisms that control Fe homeostasis in plants, major advances toward engineering biofortified crops have been made during the past decade. Examples of successful biofortification strategies are, however, still scarce and the process of Fe loading into seeds is far from being well understood in most crop species. In particular in grains where the embryo represents the main storage compartment such as legumes, increasing the seed Fe content remains a challenging task. This review aims at placing the recently identified actors in Fe transport into the unsolved puzzle of grain filling, taking the differences of Fe distribution between various species into consideration. We summarize the current knowledge on Fe transport between symplasmic and apoplasmic compartments, and provide models for Fe trafficking and localization in different seed types that may help to develop high seed Fe germplasms.
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Affiliation(s)
- Louis Grillet
- Institute of Plant and Microbial BiologyAcademia Sinica, Taipei, Taiwan
| | - Stéphane Mari
- Plant Biology, Institut National pour la Recherche AgronomiqueMontpellier, France
| | - Wolfgang Schmidt
- Institute of Plant and Microbial BiologyAcademia Sinica, Taipei, Taiwan
- *Correspondence: Wolfgang Schmidt, Institute of Plant and Microbial Biology, Academia Sinica, Academia Road 128, Taipei 11529, Taiwan e-mail:
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19
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Xiang Q, Wang Z, Zhang Y, Wang H. An oligopeptide transporter gene family in Phanerochaete chrysosporium. Gene 2013; 522:133-41. [DOI: 10.1016/j.gene.2013.03.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 02/21/2013] [Accepted: 03/16/2013] [Indexed: 10/27/2022]
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20
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Roles of different peptide transporters in nutrient acquisition in Candida albicans. EUKARYOTIC CELL 2013; 12:520-8. [PMID: 23376942 DOI: 10.1128/ec.00008-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Fungi possess two distinct proton-coupled peptide transport systems, the dipeptide/tripeptide transporters (PTR) and the oligopeptide transporters (OPT), which enable them to utilize peptides as nutrients. In the pathogenic yeast Candida albicans, peptide transporters are encoded by gene families consisting of two PTR genes and eight OPT genes. To gain insight into the functions and importance of specific peptide transporters, we generated mutants lacking the two dipeptide/tripeptide transporters Ptr2 and Ptr22, as well as the five major oligopeptide transporters Opt1 to Opt5. These mutants were unable to grow in media containing peptides as the sole nitrogen source. Forced expression of individual peptide transporters in the septuple mutants showed that Ptr2 and Ptr22 could utilize all tested dipeptides as substrates but differed in their abilities to transport specific tripeptides. Interestingly, several oligopeptide transporters, which are thought to transport peptides consisting of more than three amino acids, also mediated the uptake of tripeptides. Opt1 especially turned out to be a highly flexible transporter that enabled growth on all tripeptides tested and could even utilize a dipeptide, a function that has never been ascribed to this family of peptide transporters. Despite their inability to grow on proteins or peptides, the opt1Δ opt2Δ opt3Δ opt4Δ opt5Δ ptr2Δ ptr22Δ septuple mutants had no in vivo fitness defect in a mouse model of gastrointestinal colonization. Therefore, the nutritional versatility of C. albicans enables it to utilize alternative nitrogen sources in this host niche, which probably contributes to its success as a commensal and pathogen in mammalian hosts.
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Liu T, Zeng J, Xia K, Fan T, Li Y, Wang Y, Xu X, Zhang M. Evolutionary expansion and functional diversification of oligopeptide transporter gene family in rice. RICE (NEW YORK, N.Y.) 2012; 5:12. [PMID: 27234238 PMCID: PMC5520842 DOI: 10.1186/1939-8433-5-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 06/22/2012] [Indexed: 05/10/2023]
Abstract
BACKGROUND Oligopeptide transporters (OPTs) play important roles in the mobilization of organic nitrogenous compounds and usually associate with tissues that show signs of rapid protein hydrolysis, such as germinating seeds and senescing leaves. This study is to investigate rice OPT genes. RESULTS A total of sixteen OsOPT genes (Os for Oryza sative L.) were identified in the rice genome, which were then classified into six sections that belong to two subfamilies (the PT and YSL subfamily). The major mechanisms for evolutionary expansion of the sixteen genes during the rice genome evolution include segmental and tandem duplication. Calculation of the duplication event dates indicated that the sixteen genes originated from nine original OsOPT genes, and the duplication events could be classified into three evolutionary stages. The first evolutionary stage occurred approximately 50 million years ago (Mya) and involved the evolution of four new genes. The second evolutionary stage was approximately 20 Mya and was marked by the appearance of two new genes, and the third evolutionary stage was approximately 9 Mya when two new genes evolved. Mining of the expression database and RT-PCR analysis indicated that the expression of most duplicated OsOPT genes showed high tissue specificities. Diverse expression patterns for the sixteen genes were evaluated using both semi-quantitative RT-PCR and the MPSS data. Expression levels of some OsOPT genes were regulated by abiotic and biotic stresses suggesting the potential involvement of these gene products in rice stress adaptation. Five OsOPT gene mutants showed abnormal development and growth, the primary analysis of five OsOPT gene mutants suggested that they may be necessary for rice development. CONCLUSIONS These results suggested that rice-specific OsOPT genes might be potentially useful in improving rice.
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Affiliation(s)
- Tao Liu
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 People's Republic of China
| | - Jiqing Zeng
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Kuaifei Xia
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Tian Fan
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Graduate University of Chinese Academy of Sciences, Beijing, 100049 People's Republic of China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Yaqin Wang
- Guangdong Key Lab of Biotechnology for Plant Development, College of Life Science, South China Normal University, Guangzhou, 510631 People's Republic of China
| | - Xinlan Xu
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650 People's Republic of China
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Hu YT, Ming F, Chen WW, Yan JY, Xu ZY, Li GX, Xu CY, Yang JL, Zheng SJ. TcOPT3, a member of oligopeptide transporters from the hyperaccumulator Thlaspi caerulescens, is a novel Fe/Zn/Cd/Cu transporter. PLoS One 2012; 7:e38535. [PMID: 22761683 PMCID: PMC3382247 DOI: 10.1371/journal.pone.0038535] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Accepted: 05/06/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Thlaspi caerulescens is a natural selected heavy metal hyperaccumulator that can not only tolerate but also accumulate extremely high levels of heavy metals in the shoots. Thus, to identify the transportors involved in metal long-distance transportation is very important for understanding the mechanism of heavy metal accumulation in this hyperaccumulator. METHODOLOGY/PRINCIPAL FINDINGS We cloned and characterized a novel gene TcOPT3 of OPT family from T. caerulescens. TcOPT3 was pronouncedly expressed in aerial parts, including stem and leaf. Moreover, in situ hybridization analyses showed that TcOPT3 expressed in the plant vascular systems, especially in the pericycle cells that may be involved in the long-distance transportation. The expression of TcOPT3 was highly induced by iron (Fe) and zinc (Zn) deficiency, especially in the stem and leaf. Sub-cellular localization showed that TcOPT3 was a plasma membrane-localized protein. Furthermore, heterogonous expression of TcOPT3 by mutant yeast (Saccharomyces cerevisiae) complementation experiments demonstrated that TcOPT3 could transport Fe(2+) and Zn(2+). Moreover, expression of TcOPT3 in yeast increased metal (Fe, Zn, Cu and Cd) accumulation and resulted in an increased sensitivity to cadmium (Cd) and copper (Cu). CONCLUSIONS Our data demonstrated that TcOPT3 might encode an Fe/Zn/Cd/Cu influx transporter with broad-substrate. This is the first report showing that TcOPT3 may be involved in metal long-distance transportation and contribute to the heavy metal hyperaccumulation.
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Affiliation(s)
- Yi Ting Hu
- College of Environmental and Resource Sciences, Zhejiang University, Hanzhou, China
- Key Laboratory of Conservation Biology for Endangered Wildlife, Ministry of Education, College of Life Science, Zhejiang University, Hanzhou, China
| | - Feng Ming
- Institute of Plant Biology, School of Life Science, Fudan University, Shanghai, China
| | - Wei Wei Chen
- Key Laboratory of Conservation Biology for Endangered Wildlife, Ministry of Education, College of Life Science, Zhejiang University, Hanzhou, China
| | - Jing Ying Yan
- Key Laboratory of Conservation Biology for Endangered Wildlife, Ministry of Education, College of Life Science, Zhejiang University, Hanzhou, China
| | - Zheng Yu Xu
- The Anhui Provincial Lab of Nutrient Cycling, Resources and Environment; Institute of Soil and Fertilizer, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Gui Xin Li
- College of Agronomy and Biotechnology, Zhejiang University, Hanzhou, China
| | - Chun Yan Xu
- State Environmental Protection Administration of Radiation Environmental Monitoring Technology Center, Hanghzou, China
| | - Jian Li Yang
- Key Laboratory of Conservation Biology for Endangered Wildlife, Ministry of Education, College of Life Science, Zhejiang University, Hanzhou, China
| | - Shao Jian Zheng
- College of Environmental and Resource Sciences, Zhejiang University, Hanzhou, China
- Key Laboratory of Conservation Biology for Endangered Wildlife, Ministry of Education, College of Life Science, Zhejiang University, Hanzhou, China
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The Ubiquitin ligase Ubr11 is essential for oligopeptide utilization in the fission yeast Schizosaccharomyces pombe. EUKARYOTIC CELL 2012; 11:302-10. [PMID: 22226946 DOI: 10.1128/ec.05253-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Uptake of extracellular oligopeptides in yeast is mediated mainly by specific transporters of the peptide transporter (PTR) and oligopeptide transporter (OPT) families. Here, we investigated the role of potential peptide transporters in the yeast Schizosaccharomyces pombe. Utilization of naturally occurring dipeptides required only Ptr2/SPBC13A2.04c and none of the other 3 OPT proteins (Isp4, Pgt1, and Opt3), whereas only Isp4 was indispensable for tetrapeptide utilization. Both Ptr2 and Isp4 localized to the cell surface, but under rich nutrient conditions Isp4 localized in the Golgi apparatus through the function of the ubiquitin ligase Pub1. Furthermore, the ubiquitin ligase Ubr11 played a significant role in oligopeptide utilization. The mRNA levels of both the ptr2 and isp4 genes were significantly reduced in ubr11Δ cells, and the dipeptide utilization defect in the ubr11Δ mutant was rescued by the forced expression of Ptr2. Consistent with its role in transcriptional regulation of peptide transporter genes, the Ubr11 protein was accumulated in the nucleus. Unlike the situation in Saccharomyces cerevisiae, the oligopeptide utilization defect in the S. pombe ubr11Δ mutant was not rescued by inactivation of the Tup11/12 transcriptional corepressors, suggesting that the requirement for the Ubr ubiquitin ligase in the upregulation of peptide transporter mRNA levels is conserved in both yeasts; however, the actual mechanism underlying the control appears to be different. We also found that the peptidomimetic proteasome inhibitor MG132 was still operative in a strain lacking all known PTR and OPT peptide transporters. Therefore, irrespective of its peptide-like structure, MG132 is carried into cells independently of the representative peptide transporters.
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Hartmann T, Cairns TC, Olbermann P, Morschhäuser J, Bignell EM, Krappmann S. Oligopeptide transport and regulation of extracellular proteolysis are required for growth of Aspergillus fumigatus on complex substrates but not for virulence. Mol Microbiol 2011; 82:917-35. [DOI: 10.1111/j.1365-2958.2011.07868.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Desai PR, Thakur A, Ganguli D, Paul S, Morschhäuser J, Bachhawat AK. Glutathione utilization by Candida albicans requires a functional glutathione degradation (DUG) pathway and OPT7, an unusual member of the oligopeptide transporter family. J Biol Chem 2011; 286:41183-41194. [PMID: 21994941 DOI: 10.1074/jbc.m111.272377] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Candida albicans lacks the ability to survive within its mammalian host in the absence of endogenous glutathione biosynthesis. To examine the ability of this yeast to utilize exogenous glutathione, we exploited the organic sulfur auxotrophy of C. albicans met15Δ strains. We observed that glutathione is utilized efficiently by the alternative pathway of glutathione degradation (DUG pathway). The major oligopeptide transporters OPT1-OPT5 of C. albicans that were most similar to the known yeast glutathione transporters were not found to contribute to glutathione transport to any significant extent. A genomic library approach to identify the glutathione transporter of C. albicans yielded OPT7 as the primary glutathione transporter. Biochemical studies on OPT7 using radiolabeled GSH uptake revealed a K(m) of 205 μm, indicating that it was a high affinity glutathione transporter. OPT7 is unusual in several aspects. It is the most remote member to known yeast glutathione transporters, lacks the two highly conserved cysteines in the family that are known to be crucial in trafficking, and also has the ability to take up tripeptides. The transporter was regulated by sulfur sources in the medium. OPT7 orthologues were prevalent among many pathogenic yeasts and fungi and formed a distinct cluster quite remote from the Saccharomyces cerevisiae HGT1 glutathione transporter cluster. In vivo experiments using a systemic model of candidiasis failed to detect expression of OPT7 in vivo, and strains disrupted either in the degradation (dug3Δ) or transport (opt7Δ) of glutathione failed to show a defect in virulence.
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Affiliation(s)
- Prashant Ramesh Desai
- Institute of Microbial Technology (Council for Scientific and Industrial Research), Chandigarh 160036, India
| | - Anil Thakur
- Institute of Microbial Technology (Council for Scientific and Industrial Research), Chandigarh 160036, India
| | - Dwaipayan Ganguli
- Institute of Microbial Technology (Council for Scientific and Industrial Research), Chandigarh 160036, India
| | - Sanjoy Paul
- Institute of Microbial Technology (Council for Scientific and Industrial Research), Chandigarh 160036, India
| | - Joachim Morschhäuser
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, 97080 Würzburg, Germany
| | - Anand K Bachhawat
- Institute of Microbial Technology (Council for Scientific and Industrial Research), Chandigarh 160036, India; Indian Institute of Science Education & Research Mohali, Knowledge City, S.A.S. Nagar, Punjab-140306, India.
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Cao J, Huang J, Yang Y, Hu X. Analyses of the oligopeptide transporter gene family in poplar and grape. BMC Genomics 2011; 12:465. [PMID: 21943393 PMCID: PMC3188535 DOI: 10.1186/1471-2164-12-465] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2011] [Accepted: 09/26/2011] [Indexed: 11/12/2022] Open
Abstract
Background Oligopeptide transporters (OPTs) are a group of membrane-localized proteins that have a broad range of substrate transport capabilities and that are thought to contribute to many biological processes. The OPT proteins belong to a small gene family in plants, which includes about 25 members in Arabidopsis and rice. However, no comprehensive study incorporating phylogeny, chromosomal location, gene structure, expression profiling, functional divergence and selective pressure analysis has been reported thus far for Populus and Vitis. Results In the present study, a comprehensive analysis of the OPT gene family in Populus (P. trichocarpa) and Vitis (V. vinifera) was performed. A total of 20 and 18 full-length OPT genes have been identified in Populus and Vitis, respectively. Phylogenetic analyses indicate that these OPT genes consist of two classes that can be further subdivided into 11 groups. Gene structures are considerably conserved among the groups. The distribution of OPT genes was found to be non-random across chromosomes. A high proportion of the genes are preferentially clustered, indicating that tandem duplications may have contributed significantly to the expansion of the OPT gene family. Expression patterns based on our analyses of microarray data suggest that many OPT genes may be important in stress response and functional development of plants. Further analyses of functional divergence and adaptive evolution show that, while purifying selection may have been the main force driving the evolution of the OPTs, some of critical sites responsible for the functional divergence may have been under positive selection. Conclusions Overall, the data obtained from our investigation contribute to a better understanding of the complexity of the Populus and Vitis OPT gene family and of the function and evolution of the OPT gene family in higher plants.
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Affiliation(s)
- Jun Cao
- Key Laboratory of Biodiversity and Biogeography, Kunming Institute of Botany, Institute of Tibet Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650204, China
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Lubkowitz M. The oligopeptide transporters: a small gene family with a diverse group of substrates and functions? MOLECULAR PLANT 2011; 4:407-15. [PMID: 21310763 DOI: 10.1093/mp/ssr004] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Genes in the Oligopeptide Transport family encode integral membrane proteins that are believed to translocate their substrates from either the extracellular environment or an organelle into the cytosol. Phylogenetic analyses of plant transporters have revealed two distant clades: the Yellow Stripe-Like (YSL) proteins and the so-called Oligopeptide Transporters (OPTs), for which the family was named. Three categories of substrates have been identified for this family: small peptides, secondary amino acids bound to metals, and glutathione. Notably, the YSL transporters are involved in metal homeostasis through the translocation of metal-chelates, indicating a level of conservation both in biological function as well as substrates. In contrast, the functions of OPT proteins seem to be less defined and, in this review, I will examine the supporting and contradictory evidence for the proposed roles of OPTs in such diverse functions as long-distance sulfur distribution, nitrogen mobilization, metal homeostasis, and heavy metal sequestration through the transport of glutathione, metal-chelates, and peptides.
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Affiliation(s)
- Mark Lubkowitz
- Department of Biology, Saint Michael's College, 1 Winooski Park, Colchester, VT 05439, USA.
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Sriranganadane D, Waridel P, Salamin K, Reichard U, Grouzmann E, Neuhaus JM, Quadroni M, Monod M. Aspergillus protein degradation pathways with different secreted protease sets at neutral and acidic pH. J Proteome Res 2010; 9:3511-9. [PMID: 20486678 DOI: 10.1021/pr901202z] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aspergillus fumigatus grows well at neutral and acidic pH in a medium containing protein as the sole nitrogen source by secreting two different sets of proteases. Neutral pH favors the secretion of neutral and alkaline endoproteases, leucine aminopeptidases (Laps) which are nonspecific monoaminopeptidases, and an X-prolyl dipeptidase (DppIV). Acidic pH environment promotes the secretion of an aspartic endoprotease of pepsin family (Pep1) and tripeptidyl-peptidases of the sedolisin family (SedB and SedD). A novel prolyl peptidase, AfuS28, was found to be secreted in both alkaline and acidic conditions. In previous studies, Laps were shown to degrade peptides from their N-terminus until an X-Pro sequence acts as a stop signal. X-Pro sequences can be then removed by DppIV, which allows Laps access to the following residues. We have shown that at acidic pH Seds degrade large peptides from their N-terminus into tripeptides until Pro in P1 or P'1 position acts as a stop for these exopeptidases. However, X-X-Pro and X-X-X-Pro sequences can be removed by AfuS28 thus allowing Seds further sequential proteolysis. In conclusion, both alkaline and acidic sets of proteases contain exoprotease activity capable of cleaving after proline residues that cannot be removed during sequential digestion by nonspecific exopeptidases.
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Affiliation(s)
- Dev Sriranganadane
- Department of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
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29
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The role of transmembrane domain 9 in substrate recognition by the fungal high-affinity glutathione transporters. Biochem J 2010; 429:593-602. [DOI: 10.1042/bj20100240] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Hgt1p, a high-affinity glutathione transporter from Saccharomyces cerevisiae belongs to the recently described family of OPTs (oligopeptide transporters), the majority of whose members still have unknown substrate specificity. To obtain insights into substrate recognition and translocation, we have subjected all 21 residues of TMD9 (transmembrane domain 9) to alanine-scanning mutagenesis. Phe523 was found to be critical for glutathione recognition, since F523A mutants showed a 4-fold increase in Km without affecting expression or localization. Phe523 and the previously identified polar residue Gln526 were on the same face of the helix suggesting a joint participation in glutathione recognition, whereas two other polar residues, Ser519 and Asn522, of TMD9, although also orientated on the same face, did not appear to be involved. The size and hydrophobicity of Phe523 were both key features of its functionality, as seen from mutational analysis. Sequence alignments revealed that Phe523 and Gln526 were conserved in a cluster of OPT homologues from different fungi. A second cluster contained isoleucine and glutamate residues in place of phenylalanine and glutamine residues, residues that are best tolerated in Hgt1p for glutathione transporter activity, when introduced together. The critical nature of the residues at these positions in TMD9 for substrate recognition was exploited to assign substrate specificities of several putative fungal orthologues present in these and other clusters. The presence of either phenylalanine and glutamine or isoleucine and glutamate residues at these positions correlated with their function as high-affinity glutathione transporters based on genetic assays and the Km of these transporters towards glutathione.
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Aouida M, Khodami-Pour A, Ramotar D. Novel role for the Saccharomyces cerevisiae oligopeptide transporter Opt2 in drug detoxification. Biochem Cell Biol 2009; 87:653-61. [PMID: 19767828 DOI: 10.1139/o09-045] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Saccharomyces cerevisiae Opt2 is a member of the oligopeptide transporter family that was initially identified to transport tetra- and pentapeptides. Mutants deleted for the OPT2 gene exhibit no growth defects under normal culture conditions. We identified OPT2 from a high-throughput screen that when deleted results in mutants that displayed sensitivity to the anticancer agent bleomycin. The opt2Delta mutant was also reisolated in two additional genome-wide screens designed to identify mutants that are sensitive to the immunosuppressant rapamycin and the divalent metal ion zinc. However, the role of Opt2 in protecting cells against these agents was not investigated. Herein, we show that opt2Delta mutants are also sensitive to a wide variety of toxic agents that are typically detoxified by the vacuoles. Mutants lacking two other related oligopeptide transporters, Opt1 and Ygl114w, showed no significant sensitivities to these drugs, indicating a specific role for Opt2 in drug detoxification. The sensitivities of the opt2Delta mutants were not related to an increased drug uptake but rather to the presence of several small vesicles instead of a functional large vacuole. We propose that Opt2 has a novel function involving the fusion of vesicles to form a mature vacuole.
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Affiliation(s)
- Mustapha Aouida
- Maisonneuve-Rosemont Hospital, Research Center, 5415 Boul. de l'Assomption, Montreal, QC H1T 2M4, Canada
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31
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Pike S, Patel A, Stacey G, Gassmann W. Arabidopsis OPT6 is an oligopeptide transporter with exceptionally broad substrate specificity. PLANT & CELL PHYSIOLOGY 2009; 50:1923-32. [PMID: 19808809 DOI: 10.1093/pcp/pcp136] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Oligopeptide transporters (OPTs) are found in fungi, bacteria and plants. The nine Arabidopsis thaliana OPT genes are expressed mainly in the vasculature and are thought to transport tetra- and pentapeptides, and peptide-like substrates such as glutathione. Expression of AtOPT6 in Xenopus laevis oocytes demonstrated that AtOPT6 transports many tetra- and pentapeptides. In addition, AtOPT6 transported reduced glutathione (GSH), a tripeptide, but not oxidized glutathione (GSSG). Recent data showed that Candida albicans OPTs can transport peptides up to eight amino acids in length. AtOPT6 transported mammalian signaling peptides up to 10 amino acids in length and, in addition, known plant development- and nematode pathogenesis-associated peptides up to 13 amino acids long. AtOPT6 displayed high affinity for penta- and dodecapeptides, but low affinity for GSH. In comparison the Saccharomyces cerevisiae ScOPT1 was incapable of transporting any of the longer peptides tested. These data demonstrate the necessity of experimentally determining substrate specificity of individual OPTs, and lay a foundation for structure/function studies. Characterization of the AtOPT6 substrate range provides a basis for investigating the possible physiological function of AtOPT6 in peptide signaling and thiol transport in response to stress.
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Affiliation(s)
- Sharon Pike
- Division of Plant Sciences and Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211-7310, USA
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32
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Casagrande F, Harder D, Schenk A, Meury M, Ucurum Z, Engel A, Weitz D, Daniel H, Fotiadis D. Projection structure of DtpD (YbgH), a prokaryotic member of the peptide transporter family. J Mol Biol 2009; 394:708-17. [PMID: 19782088 DOI: 10.1016/j.jmb.2009.09.048] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Revised: 09/09/2009] [Accepted: 09/18/2009] [Indexed: 10/20/2022]
Abstract
Cellular uptake of di- and tripeptides has been characterized in numerous organisms, and various transporters have been identified. In contrast, structural information on peptide transporters is very sparse. Here, we have cloned, overexpressed, purified, and biochemically characterized DtpD (YbgH) from Escherichia coli, a prokaryotic member of the peptide transporter family. Its homologues in mammals, PEPT1 (SLC15A1) and PEPT2 (SLC15A2), not only transport peptides but also are of relevance for uptake of drugs as they accept a large spectrum of peptidomimetics such as beta-lactam antibiotics, antivirals, peptidase inhibitors, and others as substrates. Uptake experiments indicated that DtpD functions as a canonical peptide transporter and is, therefore, a valid model for structural studies of this family of proteins. Blue native polyacrylamide gel electrophoresis, gel filtration, and transmission electron microscopy of single-DtpD particles suggest that the transporter exists in a monomeric form when solubilized in detergent. Two-dimensional crystallization of DtpD yielded first tubular crystals that allowed the determination of a projection structure at better than 19 A resolution. This structure of DtpD represents the first structural view of a member of the peptide transporter family.
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Affiliation(s)
- Fabio Casagrande
- Department of Chemistry and Biochemistry, University of California, 9500 Gilman Drive, San Diego, La Jolla, CA 92093, USA
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33
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Kaur J, Bachhawat AK. Gln-222 in transmembrane domain 4 and Gln-526 in transmembrane domain 9 are critical for substrate recognition in the yeast high affinity glutathione transporter, Hgt1p. J Biol Chem 2009; 284:23872-84. [PMID: 19589778 PMCID: PMC2749159 DOI: 10.1074/jbc.m109.029728] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2009] [Revised: 07/02/2009] [Indexed: 11/06/2022] Open
Abstract
Hgt1p, a member of the oligopeptide transporter family, is a high affinity glutathione transporter from the yeast Saccharomyces cerevisiae. We have explored the role of polar or charged residues in the putative transmembrane domains of Hgt1p to obtain insights into the structural features of Hgt1p that govern its substrate specificity. A total of 22 charged and polar residues in the predicted transmembrane domains and other conserved regions were subjected to alanine mutagenesis. Functional characterization of these 22 mutants identified 11 mutants which exhibited significant loss in functional activity. All 11 mutants except T114A had protein expression levels comparable with wild type, and all except E744A were proficient in trafficking to the cell surface. Kinetic analyses revealed differential contributions toward the functional activity of Hgt1p by these residues and identified Asn-124 in transmembrane domain 1 (TMD1), Gln-222 in TMD4, Gln-526 in TMD9, and Glu-544, Arg-554, and Lys-562 in the intracellular loop region 537-568 containing the highly conserved proline-rich motif to be essential for the transport activity of the protein. Furthermore, mutants Q222A and Q526A exhibited a nearly 4- and 8-fold increase in the K(m) for glutathione. Interestingly, although Gln-222 is widely conserved among other functionally characterized oligopeptide transporter family members including those having a different substrate specificity, Gln-526 is present only in Hgt1p and Pgt1, the only two known high affinity glutathione transporters. These results provide the first insights into the substrate recognition residues of a high affinity glutathione transporter and on residues/helices involved in substrate translocation in the structurally uncharacterized oligopeptide transporter family.
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Affiliation(s)
- Jaspreet Kaur
- From the Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
| | - Anand K. Bachhawat
- From the Institute of Microbial Technology, Sector 39-A, Chandigarh 160 036, India
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34
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Chagué V, Maor R, Sharon A. CgOpt1, a putative oligopeptide transporter from Colletotrichum gloeosporioides that is involved in responses to auxin and pathogenicity. BMC Microbiol 2009; 9:173. [PMID: 19698103 PMCID: PMC2769210 DOI: 10.1186/1471-2180-9-173] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2008] [Accepted: 08/21/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND The fungus Colletotrichum gloeosporioides f. sp. aeschynomene produces high levels of indole-3-acetic acid (IAA) in axenic cultures and during plant infection. We generated a suppression subtractive hybridization library enriched for IAA-induced genes and identified a clone, which was highly expressed in IAA-containing medium. RESULTS The corresponding gene showed similarity to oligopeptide transporters of the OPT family and was therefore named CgOPT1. Expression of CgOPT1 in mycelia was low, and was enhanced by external application of IAA. cgopt1-silenced mutants produced less spores, had reduced pigmentation, and were less pathogenic to plants than the wild-type strain. IAA enhanced spore formation and caused changes in colony morphology in the wild-type strain, but had no effect on spore formation or colony morphology of the cgopt1-silenced mutants. CONCLUSION Our results show that IAA induces developmental changes in C. gloeosporioides. These changes are blocked in cgopt1-silenced mutants, suggesting that this protein is involved in regulation of fungal response to IAA. CgOPT1 is also necessary for full virulence, but it is unclear whether this phenotype is related to auxin.
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Affiliation(s)
- Véronique Chagué
- Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel
| | - Rudy Maor
- Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel
- Current address: Rosetta Genomics, 10 Plaut Street, Rehovot, 76706, Israel
| | - Amir Sharon
- Department of Plant Sciences, Tel Aviv University, Tel Aviv 69978, Israel
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Hauser M, Narita V, Donhardt AM, Naider F, Becker JM. Multiplicity and regulation of genes encoding peptide transporters inSaccharomyces cerevisiae. Mol Membr Biol 2009. [DOI: 10.1080/09687680010029374] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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36
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Dworeck T, Wolf K, Zimmermann M. SpOPT1, a member of the oligopeptide family (OPT) of the fission yeast Schizosaccharomyces pombe, is involved in the transport of glutathione through the outer membrane of the cell. Yeast 2009; 26:67-73. [PMID: 19180638 DOI: 10.1002/yea.1652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
A protein involved in the transport of glutathione has been identified, cloned and characterized from the fission yeast Schizosaccharomyces pombe. Database searches revealed the Sz. pombe ORF SPAC29B12.10c as a close homologue to several members of the OPT family, including the Saccharomyces cerevisiae high-affinity glutathione transporter Hgt1p. The gene product of SPAC29B12.10c has been identified as a protein, named SpOPT1, localized within the plasma membrane, transporting the tripeptide glutathione. Disruption of SPAC29B12.10c led to strains inable to grow on media containing glutathione as a sole source of sulphur, due to the inability to internalize the tripeptide. Disruptants contained significantly less glutathione than wild-type cells. Furthermore, DeltaSpopt1 strains were non-viable in a glutathione biosynthesis-defective (Deltagsh2) background. However, it was possible to complement the disruption of Spopt1 by overexpressing the intact ORF in the disrupted strain.
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Affiliation(s)
- Tamara Dworeck
- Institute of Biology IV (Microbiology and Genetics), RWTH Aachen University, Worringer Weg, D-52056 Aachen, Germany
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37
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Thakur A, Kaur J, Bachhawat AK. Pgt1, a glutathione transporter from the fission yeastSchizosaccharomyces pombe. FEMS Yeast Res 2008; 8:916-29. [DOI: 10.1111/j.1567-1364.2008.00423.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Stacey MG, Patel A, McClain WE, Mathieu M, Remley M, Rogers EE, Gassmann W, Blevins DG, Stacey G. The Arabidopsis AtOPT3 protein functions in metal homeostasis and movement of iron to developing seeds. PLANT PHYSIOLOGY 2008; 146:589-601. [PMID: 18083798 PMCID: PMC2245856 DOI: 10.1104/pp.107.108183] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Accepted: 11/25/2007] [Indexed: 05/18/2023]
Abstract
The Arabidopsis thaliana AtOPT3 belongs to the oligopeptide transporter (OPT) family, a relatively poorly characterized family of peptide/modified peptide transporters found in archebacteria, bacteria, fungi, and plants. A null mutation in AtOPT3 resulted in embryo lethality, indicating an essential role for AtOPT3 in embryo development. In this article, we report on the isolation and phenotypic characterization of a second AtOPT3 mutant line, opt3-2, harboring a T-DNA insertion in the 5' untranslated region of AtOPT3. The T-DNA insertion in the AtOPT3 promoter resulted in reduced but sufficient AtOPT3 expression to allow embryo formation in opt3-2 homozygous seeds. Phenotypic analyses of opt3-2 plants revealed three interesting loss-of-function phenotypes associated with iron metabolism. First, reduced AtOPT3 expression in opt3-2 plants resulted in the constitutive expression of root iron deficiency responses regardless of exogenous iron supply. Second, deregulation of root iron uptake processes in opt3-2 roots resulted in the accumulation of very high levels of iron in opt3-2 tissues. Hyperaccumulation of iron in opt3-2 resulted in the formation of brown necrotic areas in opt3-2 leaves and was more pronounced during the seed-filling stage. Third, reduced AtOPT3 expression resulted in decreased accumulation of iron in opt3-2 seeds. The reduced accumulation of iron in opt3-2 seeds is especially noteworthy considering the excessively high levels of accumulated iron in other opt3-2 tissues. AtOPT3, therefore, plays a critical role in two important aspects of iron metabolism, namely, maintenance of whole-plant iron homeostasis and iron nutrition of developing seeds.
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Affiliation(s)
- Minviluz G Stacey
- Division of Plant Sciences, University of Missouri, Columbia, Missouri 65211, USA
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39
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Cai H, Hauser M, Naider F, Becker JM. Differential regulation and substrate preferences in two peptide transporters of Saccharomyces cerevisiae. EUKARYOTIC CELL 2007; 6:1805-13. [PMID: 17693598 PMCID: PMC2043388 DOI: 10.1128/ec.00257-06] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Dal5p has been shown previously to act as an allantoate/ureidosuccinate permease and to play a role in the utilization of certain dipeptides as a nitrogen source in Saccharomyces cerevisiae. Here, we provide direct evidence that dipeptides are transported by Dal5p, although the affinity of Dal5p for allantoate and ureidosuccinate is higher than that for dipeptides. Allantoate, ureidosuccinate, and to a lesser extent allantoin competed with dipeptide transport by reducing the toxicity of the peptide Ala-Eth and decreasing the accumulation of [(14)C]Gly-Leu. In contrast to the well-studied di/tripeptide transporter Ptr2p, whose substrate specificity is very broad, Dal5p preferred to transport non-N-end rule dipeptides. S. cerevisiae W303 was sensitive to the toxic peptide Ala-Eth (non-N-end rule peptide) but not Leu-Eth (N-end rule peptide). Non-N-end rule dipeptides showed better competition with the uptake of [(14)C]Gly-Leu than N-end rule dipeptides. Similar to the regulation of PTR2, DAL5 expression was influenced by the addition of Leu and by the CUP9 gene. However, DAL5 expression was downregulated in the presence of leucine and the absence of CUP9, whereas PTR2 was upregulated. Toxic dipeptide and uptake assays indicated that either Ptr2p or Dal5p was predominantly used for dipeptide transport in the common laboratory strains S288c and W303, respectively. These studies highlight the complementary activities of two dipeptide transport systems under different regulatory controls in common laboratory yeast strains, suggesting that dipeptide transport pathways evolved to respond to different environmental conditions.
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Affiliation(s)
- Houjian Cai
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996-0845, USA
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Tsay YF, Chiu CC, Tsai CB, Ho CH, Hsu PK. Nitrate transporters and peptide transporters. FEBS Lett 2007; 581:2290-300. [PMID: 17481610 DOI: 10.1016/j.febslet.2007.04.047] [Citation(s) in RCA: 334] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2007] [Revised: 04/17/2007] [Accepted: 04/20/2007] [Indexed: 11/17/2022]
Abstract
In higher plants, two types of nitrate transporters, NRT1 and NRT2, have been identified. In Arabidopsis, there are 53 NRT1 genes and 7 NRT2 genes. NRT2 are high-affinity nitrate transporters, while most members of the NRT1 family are low-affinity nitrate transporters. The exception is CHL1 (AtNRT1.1), which is a dual-affinity nitrate transporter, its mode of action being switched by phosphorylation and dephosphorylation of threonine 101. Two of the NRT1 genes, CHL1 and AtNRT1.2, and two of the NRT2 genes, AtNRT2.1 and AtNRT2.2, are known to be involved in nitrate uptake. In addition, AtNRT1.4 is required for petiole nitrate storage. On the other hand, some members of the NRT1 family are dipeptide transporters, called PTRs, which transport a broad spectrum of di/tripeptides. In barley, HvPTR1, expressed in the plasma membrane of scutellar epithelial cells, is involved in mobilizing peptides, produced by hydrolysis of endosperm storage protein, to the developing embryo. In higher plants, there is another family of peptide transporters, called oligopeptide transporters (OPTs), which transport tetra/pentapeptides. In addition, some OPTs transport GSH, GSSH, GSH conjugates, phytochelatins, and metals.
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Affiliation(s)
- Yi-Fang Tsay
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan.
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Wiles AM, Cai H, Naider F, Becker JM. Nutrient regulation of oligopeptide transport in Saccharomyces cerevisiae. MICROBIOLOGY-SGM 2007; 152:3133-3145. [PMID: 17005992 DOI: 10.1099/mic.0.29055-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Small peptides (2-5 amino acid residues) are transported into Saccharomyces cerevisiae via two transport systems: PTR (Peptide TRansport) for di-/tripeptides and OPT (OligoPeptide Transport) for oligopeptides of 4-5 amino acids in length. Although regulation of the PTR system has been studied in some detail, neither the regulation of the OPT family nor the environmental conditions under which family members are normally expressed have been well studied in S. cerevisiae. Using a lacZ reporter gene construct fused to 1 kb DNA from upstream of the genes OPT1 and OPT2, which encode the two S. cerevisiae oligopeptide transporters, the relative expression levels of these genes were measured in a variety of environmental conditions. Uptake assays were also conducted to measure functional protein levels at the plasma membrane. It was found that OPT1 was up-regulated in sulfur-free medium, and that Ptr3p and Ssy1p, proteins involved in regulating the di-/tripeptide transporter encoding gene PTR2 via amino acid sensing, were required for OPT1 expression in a sulfur-free environment. In contrast, as measured by response to toxic tetrapeptide and by real-time PCR, OPT1 was not regulated through Cup9p, which is a repressor for PTR2 expression, although Cup9p did repress OPT2 expression. In addition, all of the 20 naturally occurring amino acids, except the sulfur-containing amino acids methionine and cysteine, up-regulated OPT1, with the greatest change in expression observed when cells were grown in sulfur-free medium. These data demonstrate that regulation of the OPT system has both similarities and differences to regulation of the PTR system, allowing the yeast cell to adapt its utilization of small peptides to various environmental conditions.
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Affiliation(s)
- Amy M Wiles
- Department of Biochemistry, Cell and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Houjian Cai
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
| | - Fred Naider
- Department of Chemistry, College of Staten Island, CUNY, Staten Island, NY 10301, USA
| | - Jeffrey M Becker
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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Ribichich KF, Georg RC, Gomes SL. Comparative EST analysis provides insights into the basal aquatic fungus Blastocladiella emersonii. BMC Genomics 2006; 7:177. [PMID: 16836762 PMCID: PMC1550239 DOI: 10.1186/1471-2164-7-177] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2006] [Accepted: 07/12/2006] [Indexed: 11/23/2022] Open
Abstract
Background Blastocladiella emersonii is an aquatic fungus of the Chytridiomycete class, which is at the base of the fungal phylogenetic tree. In this sense, some ancestral characteristics of fungi and animals or fungi and plants could have been retained in this aquatic fungus and lost in members of late-diverging fungal species. To identify in B. emersonii sequences associated with these ancestral characteristics two approaches were followed: (1) a large-scale comparative analysis between putative unigene sequences (uniseqs) from B. emersonii and three databases constructed ad hoc with fungal proteins, animal proteins and plant unigenes deposited in Genbank, and (2) a pairwise comparison between B. emersonii full-length cDNA sequences and their putative orthologues in the ascomycete Neurospora crassa and the basidiomycete Ustilago maydis. Results Comparative analyses of B. emersonii uniseqs with fungi, animal and plant databases through the two approaches mentioned above produced 166 B. emersonii sequences, which were identified as putatively absent from other fungi or not previously described. Through these approaches we found: (1) possible orthologues of genes previously identified as specific to animals and/or plants, and (2) genes conserved in fungi, but with a large difference in divergence rate in B. emersonii. Among these sequences, we observed cDNAs encoding enzymes from coenzyme B12-dependent propionyl-CoA pathway, a metabolic route not previously described in fungi, and validated their expression in Northern blots. Conclusion Using two different approaches involving comparative sequence analyses, we could identify sequences from the early-diverging fungus B. emersonii previously considered specific to animals or plants, and highly divergent sequences from the same fungus relative to other fungi.
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Affiliation(s)
- Karina F Ribichich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil
| | - Raphaela C Georg
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil
| | - Suely L Gomes
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes 748, São Paulo, SP 05508-000, Brazil
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Reuss O, Morschhäuser J. A family of oligopeptide transporters is required for growth of Candida albicans on proteins. Mol Microbiol 2006; 60:795-812. [PMID: 16629678 DOI: 10.1111/j.1365-2958.2006.05136.x] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The human fungal pathogen Candida albicans can use proteins as the sole source of nitrogen for growth. The secretion of aspartic proteinases, which have been shown to contribute to virulence of C. albicans, allows the fungus to digest host proteins to produce peptides that must be taken up into the cell by specific transporters. To understand in more detail how C. albicans utilizes proteins as a nitrogen source, we undertook a comprehensive analysis of oligopeptide transporters encoded in the C. albicans genome. We identified eight OPT genes encoding putative oligopeptide transporters, almost all of which are represented by polymorphic alleles in strain SC5314. Expression of these genes was differentially induced when C. albicans was grown in YCB-BSA medium, which contains bovine serum albumin as the sole nitrogen source. Whereas deletion of single OPT genes in strain SC5314 did not affect its ability to utilize proteins as a nitrogen source, opt123delta triple mutants had a severe growth defect in YCB-BSA which was rescued by reintroduction of a single copy of OPT1, OPT2 or OPT3. In addition, forced expression of OPT4 or OPT5 under control of the ADH1 promoter also restored growth of an opt123delta mutant, demonstrating that at least OPT1-OPT5 encode functional peptide transporters. The various oligopeptide transporters differ in their substrate preferences, as shown by the ability of strains expressing specific OPT genes to grow on peptides of defined length and sequence. We present evidence that in addition to the known role of oligopeptide transporters in the uptake of tetra- and pentapeptides these proteins can also transport longer peptides up to at least eight amino acids in length, ensuring an efficient utilization of the various peptides produced via endoproteolytic digestion of proteins by the secreted aspartic proteinases. As even transporters encoded by polymorphic alleles of a single gene exhibited differences in their efficiency to take up specific peptides, the oligopeptide transporters represent an example for how the evolution of gene families containing differentially expressed and functionally optimized members increases the nutritional versatility and, presumably, the adaptation of C. albicans to different host niches.
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Affiliation(s)
- Oliver Reuss
- Institut für Molekulare Infektionsbiologie, Universität Würzburg, Röntgenring 11, D-97070 Würzburg, Germany
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WATERWORTH WANDAM, BRAY CLIFFORDM. Enigma variations for peptides and their transporters in higher plants. ANNALS OF BOTANY 2006; 98:1-8. [PMID: 16735405 PMCID: PMC2803549 DOI: 10.1093/aob/mcl099] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
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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Wiles AM, Naider F, Becker JM. Transmembrane domain prediction and consensus sequence identification of the oligopeptide transport family. Res Microbiol 2006; 157:395-406. [PMID: 16364604 DOI: 10.1016/j.resmic.2005.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2005] [Revised: 10/06/2005] [Accepted: 10/07/2005] [Indexed: 11/25/2022]
Abstract
Few polytopic membrane proteins have had their topology determined experimentally. Often, researchers turn to an algorithm to predict where the transmembrane domains might lie. Here we use a consensus method, using six different transmembrane domain prediction algorithms on six members of the oligopeptide transport family, all of which have been experimentally characterized. PSI-BLAST results indicate that the six chosen oligopeptide transport family members are distributed throughout most branches of the phylogram, suggesting that these members represent a broad view of the oligopeptide transport family. We combined the prediction algorithms with a multiple sequence alignment, and consensus transmembrane domains were assigned not only based on algorithmic output, but also based on conserved familial motifs found by analysis of the PSI-BLAST results. The consensus method combined with the "charge-difference rule" yields a model topology for the family containing 12 transmembrane domains with the N- and C-termini facing extracellular.
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Affiliation(s)
- Amy M Wiles
- Department of Microbiology, University of Tennessee, Knoxville, TN 37996, USA
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Osawa H, Stacey G, Gassmann W. ScOPT1 and AtOPT4 function as proton-coupled oligopeptide transporters with broad but distinct substrate specificities. Biochem J 2006; 393:267-75. [PMID: 16149917 PMCID: PMC1383685 DOI: 10.1042/bj20050920] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A group of OPTs (oligopeptide transporters) exclusively identified in plants and fungi are proposed to transport oligopeptides and derivatives of three to six amino acids in length, but their transport mechanisms and biological functions are poorly understood. We expressed the Saccharomyces cerevisiae (yeast) OPT ScOPT1 and five Arabidopsis thaliana AtOPTs in Xenopus laevis oocytes for two-electrode voltage-clamp studies. ScOPT1 produced inward currents in response to GSH or GSSG, the phytochelatin (PC) PC2 and oligopeptides including the tetrapeptide GGFL, but not KLGL. Inward currents were dependent on the external proton and substrate concentrations, with high affinity for both. This and the inward currents evoked by substrates with net negative charges showed that ScOPT1 is a proton-coupled transporter. ScOPT1 displayed highest apparent affinity for PC2, with small differences in the maximal current among substrates. Glutathione transport by any of the tested AtOPTs, including AtOPT6, was not detected in yeast growth complementation assays. With AtOPT4, initially only small KLGL-dependent currents were recorded in batches of oocytes showing high ScOPT1 expression. AtOPT4 expression was optimized by swapping the 5'-untranslated region with that of ScOPT1. AtOPT4 displayed a higher affinity for KLGL than ScOPT1 did for any peptide. AtOPT4-mediated KLGL transport was detectable at pH 5.0, but not at pH 6.0 or 7.0. Taken together, our results demonstrate that ScOPT1 and AtOPT4 are proton-coupled OPTs with broad but distinct substrate specificities and affinities.
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Affiliation(s)
- Hiroki Osawa
- *Division of Plant Sciences, Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Gary Stacey
- *Division of Plant Sciences, Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- †Division of Biochemistry, Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
| | - Walter Gassmann
- *Division of Plant Sciences, Life Sciences Center, University of Missouri, Columbia, MO 65211, U.S.A
- To whom correspondence should be addressed (email )
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Stacey MG, Osawa H, Patel A, Gassmann W, Stacey G. Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. PLANTA 2006; 223:291-305. [PMID: 16151844 DOI: 10.1007/s00425-005-0087-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2005] [Accepted: 07/14/2005] [Indexed: 05/04/2023]
Abstract
AtOPT promoter-GUS fusions were constructed for six of the nine known, putative oligopeptide transporters (OPTs) in Arabidopsis thaliana and used to examine AtOPT expression at various stages of plant development. AtOPT1, AtOPT3, AtOPT4, AtOPT6 and AtOPT7 were expressed in the embryonic cotyledons prior to root radicle emergence. Except for AtOPT8, which gave weak expression, all AtOPTs were strongly expressed in post-germinative seedlings with strongest expression in vascular tissues of cotyledons and hypocotyls. Preferential expression of AtOPTs in vascular tissues was also observed in cotyledons, leaves, hypocotyls, roots, flowers, siliques, and seed funiculi of seedlings and adult plants. Differential tissue-specific expression was observed for specific AtOPTs. For example, AtOPT1, AtOPT3 and AtOPT8 were uniquely expressed in pollen. Only AtOPT1 was expressed in growing pollen tubes, while only AtOPT6 was observed in ovules. AtOPT8 was transiently expressed in seeds during early stages of embryogenesis. Iron limitation was found to enhance expression of AtOPT3. These data suggest distinct cellular roles for specific AtOPTs including nitrogen mobilization during germination and senescence, pollen tube growth, pollen and ovule development, seed formation and metal transport.
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Affiliation(s)
- Minviluz G Stacey
- Division of Plant Sciences, The University of Missouri, Columbia, MO 65211, USA
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Lubkowitz M. The OPT family functions in long-distance peptide and metal transport in plants. GENETIC ENGINEERING 2006; 27:35-55. [PMID: 16382870 DOI: 10.1007/0-387-25856-6_3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The OPT family was first described six years ago, and much progress has been made in understanding the role these transporters play in their respective organisms. Plants are the only organisms in which both YS- and PT-type transporters have been characterized, and all of these OPTs appear to be plasma membrane-bound proteins, suggesting that they import substrates from the apoplasm or the environment. YS1 is the only OPT known to translocate substrates from the rhizosphere, whereas all the other OPTs seem to function in long-distance transport of peptides or metals. The sum of all the studies covered in this review suggest the model for OPT function in plants depicted in Figure 4. Peptides, metal-NA, and metal-MAs complexes (Strategy II plants only) are loaded into the xylem stream in the root for long-distance transport. OPTs unload the xylem by importing substrates into sink tissues such as leaves and by transloading the phloem. Peptides and metal-NA complexes exit the leaf symplasmically or by importation into the phloem from the apoplasm by OPTs. The filial tissues (endosperm and embryo) are apoplasmically separated from the maternal tissues, and OPTs may also function in loading the developing seed. Similarly, seedlings are symplasmically disconnected from the endosperm and OPTs may help move nutrients to the growing plant. Much progress has been made in the last two years toward understanding OPTs in plants, although several fundamental questions remain unanswered. Namely, what is the level of redundancy? Is there any substrate overlap between YS and PT OPTs? How crucial are their respective roles? Are there additional functions beyond peptide and metal transport? Given the recent pace of discovery, we may not have to wait long to find out the answers.
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Affiliation(s)
- Mark Lubkowitz
- Biology Department, Saint Michael's College, Colchester, Vermont 05477, USA
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Benjdia M, Rikirsch E, Müller T, Morel M, Corratgé C, Zimmermann S, Chalot M, Frommer WB, Wipf D. Peptide uptake in the ectomycorrhizal fungus Hebeloma cylindrosporum: characterization of two di- and tripeptide transporters (HcPTR2A and B). THE NEW PHYTOLOGIST 2006; 170:401-10. [PMID: 16608464 DOI: 10.1111/j.1469-8137.2006.01672.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Constraints on plant growth imposed by low availability of nitrogen are a characteristic feature of ecosystems dominated by ectomycorrhizal plants. Ectomycorrhizal fungi play a key role in the N nutrition of plants, allowing their host plants to access decomposition products of dead plant and animal materials. Ectomycorrhizal plants are thus able to compensate for the low availability of inorganic N in forest ecosystems. The capacity to take up peptides, as well as the transport mechanisms involved, were analysed in the ectomycorrhizal fungus Hebeloma cylindrosporum. The present study demonstrated that H. cylindrosporum mycelium was able to take up di- and tripeptides and use them as sole N source. Two peptide transporters (HcPTR2A and B) were isolated by yeast functional complementation using an H. cylindrosporum cDNA library, and were shown to mediate dipeptide uptake. Uptake capacities and expression regulation of both genes were analysed, indicating that HcPTR2A was involved in the high-efficiency peptide uptake under conditions of limited N availability, whereas HcPTR2B was expressed constitutively.
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Affiliation(s)
- Mariam Benjdia
- ZMBP, Plant Physiology, Auf der Morgenstelle 1, 72076 Tübingen, Germany
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Martínez P, Ljungdahl PO. Divergence of Stp1 and Stp2 transcription factors in Candida albicans places virulence factors required for proper nutrient acquisition under amino acid control. Mol Cell Biol 2005; 25:9435-46. [PMID: 16227594 PMCID: PMC1265835 DOI: 10.1128/mcb.25.21.9435-9446.2005] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Candida albicans possesses a plasma membrane-localized sensor of extracellular amino acids. Here, we show that in response to amino acids, this sensor induces the proteolytic processing of two latent transcription factors, Stp1 and Stp2. Processing removes negative regulatory motifs present in the N-terminal domains of these factors. Strikingly, Stp1 and Stp2 exhibit a clear dichotomy in the genes they transactivate. The shorter active form of Stp2 activates genes required for amino acid uptake. The processed form of Stp1 activates genes required for degradation of extracellular protein and uptake of peptides, and cells lacking Stp1 do not express the secreted aspartyl protease SAP2 or the oligopeptide transporter OPT1. Consequently, stp1 null mutants are unable to grow on media with protein as the sole nitrogen source. Cells expressing the STP1* allele that encodes a protein lacking the inhibitory N-terminal domain constitutively express SAP2 and OPT1 even in the absence of extracellular proteins or peptides. Also, we show that Stp1 levels, but not Stp2 levels, are downregulated in the presence of millimolar concentrations of extracellular amino acids. These results define the hierarchy of regulatory mechanisms that differentially control two discrete pathways for the assimilation of nitrogen.
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Affiliation(s)
- Paula Martínez
- Ludwig Institute for Cancer Research, Box 240, S-171 77 Stockholm, Sweden.
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