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Blondeau K, Blaise F, Graille M, Kale SD, Linglin J, Ollivier B, Labarde A, Lazar N, Daverdin G, Balesdent MH, Choi DHY, Tyler BM, Rouxel T, van Tilbeurgh H, Fudal I. Crystal structure of the effector AvrLm4-7 of Leptosphaeria maculans reveals insights into its translocation into plant cells and recognition by resistance proteins. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:610-24. [PMID: 26082394 DOI: 10.1111/tpj.12913] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 06/02/2015] [Accepted: 06/08/2015] [Indexed: 05/13/2023]
Abstract
The avirulence gene AvrLm4-7 of Leptosphaeria maculans, the causal agent of stem canker in Brassica napus (oilseed rape), confers a dual specificity of recognition by two resistance genes (Rlm4 and Rlm7) and is strongly involved in fungal fitness. In order to elucidate the biological function of AvrLm4-7 and understand the specificity of recognition by Rlm4 and Rlm7, the AvrLm4-7 protein was produced in Pichia pastoris and its crystal structure was determined. It revealed the presence of four disulfide bridges, but no close structural analogs could be identified. A short stretch of amino acids in the C terminus of the protein, (R/N)(Y/F)(R/S)E(F/W), was well-conserved among AvrLm4-7 homologs. Loss of recognition of AvrLm4-7 by Rlm4 is caused by the mutation of a single glycine to an arginine residue located in a loop of the protein. Loss of recognition by Rlm7 is governed by more complex mutational patterns, including gene loss or drastic modifications of the protein structure. Three point mutations altered residues in the well-conserved C-terminal motif or close to the glycine involved in Rlm4-mediated recognition, resulting in the loss of Rlm7-mediated recognition. Transient expression in Nicotiana benthamiana (tobacco) and particle bombardment experiments on leaves from oilseed rape suggested that AvrLm4-7 interacts with its cognate R proteins inside the plant cell, and can be translocated into plant cells in the absence of the pathogen. Translocation of AvrLm4-7 into oilseed rape leaves is likely to require the (R/N)(Y/F)(R/S)E(F/W) motif as well as an RAWG motif located in a nearby loop that together form a positively charged region.
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Affiliation(s)
- Karine Blondeau
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Françoise Blaise
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marc Graille
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Shiv D Kale
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Juliette Linglin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Bénédicte Ollivier
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Audrey Labarde
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Noureddine Lazar
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Guillaume Daverdin
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Marie-Hélène Balesdent
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Danielle H Y Choi
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Brett M Tyler
- Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, 24061, USA
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, OR, 97331, USA
| | - Thierry Rouxel
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
| | - Herman van Tilbeurgh
- I2BC, Université Paris-Saclay, CEA, CNRS, Université Paris Sud, UMR9198, Bât 430, F-91405, Orsay, France
| | - Isabelle Fudal
- INRA, UMR 1290 INRA-AgroParisTech BIOGER, Avenue Lucien Brétignières, F-78850, Thiverval-Grignon, France
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Sakamoto K, Toyohara H. A comparative study of cellulase and hemicellulase activities of brackish water clam Corbicula japonica with those of other marine Veneroida bivalves. J Exp Biol 2009; 212:2812-8. [DOI: 10.1242/jeb.031567] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
SUMMARY
Corbicula japonica is a typical brackish water bivalve species belonging to the order Veneroida, and it is the most important inland fishery resource in Japan. Corbicula japonica has been suggested to assimilate organic matter from terrestrial plants, unlike Ruditapes philippinarum and Mactra veneriformis, which selectively assimilate organic matter of marine origin. This led us to hypothesize that C. japonica, despite being a suspension feeder, could assimilate cellulosic materials derived from terrestrial plants. In the present study, we measured cellulase and hemicellulase activities in the crystalline styles of C. japonica and other commercially important Veneroida bivalve species in Japan: Ruditapes philippinarum, Meretrix lamarckii and Meretrix lusoria. Corbicula japonica demonstrated notably higher cellulase, xylanase and β-mannanase activities than the other marine bivalves, suggesting that this species possesses a far greater biochemical capacity to break down the structural polysaccharides of plant cell walls than the other species. In contrast, the β-1,3-glucanase and pectinase activities of C. japonica were similar to or even lower than those of the others. This is possibly due to the presence of these polysaccharides in the cell walls of diatoms, a principal food of most marine bivalves. Although direct evidence is lacking, the high cellulase, xylanase and β-mannanase activities of C. japonica may result from adaptation to an upstream estuarine environment where phytoplankton and diatoms are scarce, but plant-derived substances are abundant.
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Affiliation(s)
- Kentaro Sakamoto
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
| | - Haruhiko Toyohara
- Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan
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Berntsson RPA, Alia Oktaviani N, Fusetti F, Thunnissen AMWH, Poolman B, Slotboom DJ. Selenomethionine incorporation in proteins expressed in Lactococcus lactis. Protein Sci 2009; 18:1121-7. [PMID: 19388077 DOI: 10.1002/pro.97] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Lactococcus lactis is a promising host for (membrane) protein overproduction. Here, we describe a protocol for incorporation of selenomethionine (SeMet) into proteins expressed in L. lactis. Incorporation efficiencies of SeMet in the membrane protein complex OpuA (an ABC transporter) and the soluble protein OppA, both from L. lactis, were monitored by mass spectrometry. Both proteins incorporated SeMet with high efficiencies (>90%), which greatly extends the usefulness of the expression host L. lactis for X-ray crystallography purposes. The crystal structure of ligand-free OppA was determined at 2.4 A resolution by a semiautomatic approach using selenium single-wavelength anomalous diffraction phasing.
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Affiliation(s)
- Ronnie P-A Berntsson
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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Doublié S. Production of selenomethionyl proteins in prokaryotic and eukaryotic expression systems. Methods Mol Biol 2007; 363:91-108. [PMID: 17272838 DOI: 10.1007/978-1-59745-209-0_5] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The use of selenomethionine as a phasing tool was first reported in 1990. Engineering of selenomethionyl proteins for structure determination is now routine. In fact, selenium is by far the most commonly used anomalous scatterer for multiwavelength anomalous diffraction studies. The past few years have seen new developments, which demonstrated the feasibility of expressing selenomethionyl protein in eukaryotic systems. In this chapter, the different methods available for producing selenomethionine-labeled proteins in bacteria, as well as in yeast and mammalian cells will be presented, along with tips for purifying and crystallizing selenomethionyl proteins.
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Affiliation(s)
- Sylvie Doublié
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, USA
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Ootsuka S, Saga N, Suzuki KI, Inoue A, Ojima T. Isolation and cloning of an endo-β-1,4-mannanase from Pacific abalone Haliotis discus hannai. J Biotechnol 2006; 125:269-80. [PMID: 16621092 DOI: 10.1016/j.jbiotec.2006.03.008] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Revised: 02/09/2006] [Accepted: 03/03/2006] [Indexed: 10/24/2022]
Abstract
An endo-beta-1,4-mannanase was isolated from digestive fluid of Pacific abalone, Haliotis discus hannai, by successive chromatographies on TOYPEARL CM-650M, hydroxyapatite, and TOYOPEARL HW50F. The abalone mannanase, named HdMan in the present paper, showed a molecular mass of approximately 39,000 Da on SDS-PAGE, and exhibited high hydrolyic activity on both galactomannan from locust bean gum and glucomannan from konjac at an optimal pH and temperature of 7.5 and 45 degrees C, respectively. HdMan could degrade either beta-1,4-mannan or beta-1,4-mannooligosaccharides to mannotriose and mannobiose similarly to beta-1,4-mannanases from Pomacea, Littorina, and Mytilus. In addition, HdMan could disperse the fronds of a red alga Porphyra yezoensis into cell masses consisting of 10-20 cells that are available for cell engineering of this alga. cDNAs encoding HdMan were amplified by polymerase chain reaction from an abalone-hepatopancreas cDNA library. From the nucleotide sequences of the cDNAs, the sequence of 1232 bp in total was determined and the amino-acid sequence of 377 residues was deduced from the translational region of 1134 bp locating at nucleotide positions 15-1148. The N-terminal region of 17 residues except for the initiation Met, was regarded as the signal peptide of HdMan because it was absent in the HdMan protein and showed high similarity to the consensus sequence for signal peptides of eukaryote secretory proteins. Accordingly, mature HdMan was considered to consist of 359 residues with the calculated molecular mass of 39,627.2 Da. HdMan is classified into glycoside hydrolase family 5 (GHF5) on the basis of sequence homology to GHF5 enzymes.
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Affiliation(s)
- Shuuji Ootsuka
- Laboratory of Breeding Sciences, Graduate School of Fisheries Sciences, Hokkaido University, Hakodate, Hokkaido, Japan
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Larsson AM, Anderson L, Xu B, Muñoz IG, Usón I, Janson JC, Stålbrand H, Ståhlberg J. Three-dimensional crystal structure and enzymic characterization of beta-mannanase Man5A from blue mussel Mytilus edulis. J Mol Biol 2006; 357:1500-10. [PMID: 16487541 DOI: 10.1016/j.jmb.2006.01.044] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 01/05/2006] [Accepted: 01/09/2006] [Indexed: 11/23/2022]
Abstract
Endo-beta-1,4-d-mannanase is the key depolymerizing enzyme for beta-1,4-mannan polymers present in the cell walls of plants and some algae, as well as in some types of plant seeds. Endo-1,4-beta-mannanase from blue mussel Mytilus edulis (MeMan5A) belongs to the glycoside hydrolase (GH) family 5 enzymes. The MeMan5A structure has been determined to 1.6A resolution using the multiple-wavelength anomalous dispersion method at the selenium K edge with selenomethionyl MeMan5A expressed in the yeast Pichia pastoris. As expected for GH 5 enzymes, the structure showed a (betaalpha)(8)-barrel fold. An unusually large number of histidine side-chains are exposed on the surface, which may relate to its location within the crystalline style of the digestive tract of the mussel. Kinetic analysis of MeMan5A revealed that the enzyme requires at least six subsites for efficient hydrolysis. Mannotetraose (M4) and mannopentaose (M5) were shown to interact with subsites -3 to +1, and -3 to +2, respectively. A clear kinetic threshold was observed when going from M4 to M5, indicating that the +2 subsite provides important interaction in the hydrolysis of short oligomeric mannose substrates. The catalytic centre motif at subsite -1 found in superfamily GH clan A is, as expected, conserved in MeMan5A, but the architecture of the catalytic cleft differs significantly from other GH 5 enzyme structures. We therefore suggest that MeMan5A represents a new subfamily in GH 5.
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Affiliation(s)
- Anna M Larsson
- Department of Cell and Molecular Biology, Uppsala University, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden
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Chen CY, Cheng CH, Chen YC, Lee JC, Chou SH, Huang W, Chuang WJ. Preparation of amino-acid-type selective isotope labeling of protein expressed in Pichia pastoris. Proteins 2005; 62:279-87. [PMID: 16283643 DOI: 10.1002/prot.20742] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the culture conditions for successful amino-acid-type selective (AATS) isotope labeling of protein expressed in Pichia pastoris (P. pastoris). Rhodostomin (Rho), a six disulfide-bonded protein expressed in P. pastoris with the correct fold, was used to optimize the culture conditions. The concentrations of [alpha-15N] selective amino acid, nonlabeled amino acids, and ammonium chloride, as well as induction time, were optimized to avoid scrambling and to increase the incorporation rate and protein yield. The optimized protocol was successfully applied to produce AATS isotope-labeled Rho. The labeling of [alpha-15N]Cys has a 50% incorporation rate, and all 12 cysteine resonances were observed in HSQC spectrum. The labeling of [alpha-15N]Leu, -Lys, and -Met amino acids has an incorporation rate greater than 65%, and the expected number of resonances in the HSQC spectra were observed. In contrast, the labeling of [alpha-15N]Asp and -Gly amino acids has a low incorporation rate and the scrambling problem. In addition, the culture condition was successfully applied to label dendroaspin (Den), a four disulfide-bonded protein expressed in P. pastoris. Therefore, the described condition should be generally applicable to other proteins produced in the P. pastoris expression system. This is the first report to present a protocol for AATS isotope labeling of protein expressed in P. pastoris for NMR study.
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Affiliation(s)
- Chiu-Yueh Chen
- Department of Biochemistry and Institute of Basic Medical Science, National Cheng Kung University College of Medicine, Tainan 701, Taiwan
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Strub MP, Hoh F, Sanchez JF, Strub JM, Böck A, Aumelas A, Dumas C. Selenomethionine and selenocysteine double labeling strategy for crystallographic phasing. Structure 2004; 11:1359-67. [PMID: 14604526 DOI: 10.1016/j.str.2003.09.014] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A protocol for the quantitative incorporation of both selenomethionine and selenocysteine into recombinant proteins overexpressed in Escherichia coli is described. This methodology is based on the use of a suitable cysteine auxotrophic strain and a minimal medium supplemented with selenium-labeled methionine and cysteine. The proteins chosen for these studies are the cathelin-like motif of protegrin-3 and a nucleoside-diphosphate kinase. Analysis of the purified proteins by electrospray mass spectrometry and X-ray crystallography revealed that both cysteine and methionine residues were isomorphously replaced by selenocysteine and selenomethionine. Moreover, selenocysteines allowed the formation of unstrained and stable diselenide bridges in place of the canonical disulfide bonds. In addition, we showed that NDP kinase contains a selenocysteine adduct on Cys122. This novel selenium double-labeling method is proposed as a general approach to increase the efficiency of the MAD technique used for phase determination in protein crystallography.
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Affiliation(s)
- Marie Paule Strub
- Centre de Biochimie Structurale, UMR CNRS 5048, UMR 554 INSERM, Université Montpellier I, 34090 Cedex, Montpellier, France
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