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Amkul K, Laosatit K, Lin Y, Yuan X, Chen X, Somta P. A Gene Encoding Xylanase Inhibitor Is a Candidate Gene for Bruchid ( Callosobruchus spp.) Resistance in Zombi Pea ( Vigna vexillata (L.) A. Rich). PLANTS (BASEL, SWITZERLAND) 2023; 12:3602. [PMID: 37896065 PMCID: PMC10610162 DOI: 10.3390/plants12203602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Two bruchid species, Callosobruchus maculatus and Callosobruchus chinensis, are the most significant stored insect pests of tropical legume crops. Previously, we identified a major QTL, qBr6.1, controlling seed resistance to these bruchids in the cultivated zombi pea (Vigna vexillata) accession 'TVNu 240'. In this study, we have narrowed down the qBr6.1 region and identified a candidate gene conferring this resistance. Fine mapping using F2 and F2:3 populations derived from a cross between TVNu 240 and TVNu 1623 (susceptible) revealed the existence of two tightly linked QTLs, designated qBr6.1-A and qBr6.1-B, within the qBr6.1. The QTLs qBr6.1-A and qBr6.1-B explained 37.46% and 10.63% of bruchid resistance variation, respectively. qBr6.1-A was mapped to a 28.24 kb region containing four genes, from which the gene VvTaXI encoding a xylanase inhibitor was selected as a candidate gene responsible for the resistance associated with the qBr6.1-A. Sequencing and sequence alignment of VvTaXI from TVNu 240 and TVNu 1623 revealed a 1-base-pair insertion/deletion and five single-nucleotide polymorphisms (SNPs) in the 5' UTR and 11 SNPs in the exon. Alignment of the VvTAXI protein sequences showed five amino acid changes between the TVNu 240 and TVNu 1623 sequences. Altogether, these results demonstrated that the VvTaXI encoding xylanase inhibitor is the candidate gene conferring bruchid resistance in the zombi pea accession TVNu 240. The gene VvTaXI will be useful for the molecular breeding of bruchid resistance in the zombi pea.
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Affiliation(s)
- Kitiya Amkul
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; (K.A.); (K.L.)
| | - Kularb Laosatit
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; (K.A.); (K.L.)
| | - Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (X.Y.)
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (X.Y.)
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.L.); (X.Y.)
| | - Prakit Somta
- Department of Agronomy, Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand; (K.A.); (K.L.)
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Mendonça M, Barroca M, Collins T. Endo-1,4-β-xylanase-containing glycoside hydrolase families: Characteristics, singularities and similarities. Biotechnol Adv 2023; 65:108148. [PMID: 37030552 DOI: 10.1016/j.biotechadv.2023.108148] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 04/02/2023] [Accepted: 04/04/2023] [Indexed: 04/09/2023]
Abstract
Endo-1,4-β-xylanases (EC 3.2.1.8) are O-glycoside hydrolases that cleave the internal β-1,4-D-xylosidic linkages of the complex plant polysaccharide xylan. They are produced by a vast array of organisms where they play critical roles in xylan saccharification and plant cell wall hydrolysis. They are also important industrial biocatalysts with widespread application. A large and ever growing number of xylanases with wildly different properties and functionalites are known and a better understanding of these would enable a more effective use in various applications. The Carbohydrate-Active enZYmes database (CAZy), which classifies evolutionarily related proteins into a glycoside hydrolase family-subfamily organisational scheme has proven powerful in understanding these enzymes. Nevertheless, ambiguity currently exists as to the number of glycoside hydrolase families and subfamilies harbouring catalytic domains with true endoxylanase activity and as to the specific characteristics of each of these families/subfamilies. This review seeks to clarify this, identifying 9 glycoside hydrolase families containing enzymes with endo-1,4-β-xylanase activity and discussing their properties, similarities, differences and biotechnological perspectives. In particular, substrate specificities and hydrolysis patterns and the structural determinants of these are detailed, with taxonomic aspects of source organisms being also presented. Shortcomings in current knowledge and research areas that require further clarification are highlighted and suggestions for future directions provided. This review seeks to motivate further research on these enzymes and especially of the lesser known endo-1,4-β-xylanase containing families. A better understanding of these enzymes will serve as a foundation for the knowledge-based development of process-fitted endo-1,4-β-xylanases and will accelerate their development for use with even the most recalcitrant of substrates in the biobased industries of the future.
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Cathepsins Trigger Cell Death and Regulate Radioresistance in Glioblastoma. Cells 2022; 11:cells11244108. [PMID: 36552871 PMCID: PMC9777369 DOI: 10.3390/cells11244108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022] Open
Abstract
Treatment of glioblastoma (GBM) remains very challenging, and it is particularly important to find sensitive and specific molecular targets. In this work, we reveal the relationship between the expression of cathepsins and radioresistance in GBM. We analyzed cathepsins (cathepsin B, cathepsin D, cathepsin L, and cathepsin Z/X), which are highly associated with the radioresistance of GBM by regulating different types of cell death. Cathepsins could be potential targets for GBM treatment.
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Tundo S, Mandalà G, Sella L, Favaron F, Bedre R, Kalunke RM. Xylanase Inhibitors: Defense Players in Plant Immunity with Implications in Agro-Industrial Processing. Int J Mol Sci 2022; 23:ijms232314994. [PMID: 36499321 PMCID: PMC9739030 DOI: 10.3390/ijms232314994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/17/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Xylanase inhibitors (XIs) are plant cell wall proteins largely distributed in monocots that inhibit the hemicellulose degrading activity of microbial xylanases. XIs have been classified into three classes with different structures and inhibition specificities, namely Triticum aestivum xylanase inhibitors (TAXI), xylanase inhibitor proteins (XIP), and thaumatin-like xylanase inhibitors (TLXI). Their involvement in plant defense has been established by several reports. Additionally, these inhibitors have considerable economic relevance because they interfere with the activity of xylanases applied in several agro-industrial processes. Previous reviews highlighted the structural and biochemical properties of XIs and hypothesized their role in plant defense. Here, we aimed to update the information on the genomic organization of XI encoding genes, the inhibition properties of XIs against microbial xylanases, and the structural properties of xylanase-XI interaction. We also deepened the knowledge of XI regulation mechanisms in planta and their involvement in plant defense. Finally, we reported the recently studied strategies to reduce the negative impact of XIs in agro-industrial processes and mentioned their allergenicity potential.
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Affiliation(s)
- Silvio Tundo
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
- Correspondence:
| | - Giulia Mandalà
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Luca Sella
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
| | - Francesco Favaron
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, 35020 Legnaro, Italy
| | - Renesh Bedre
- Texas A&M AgriLife Research and Extension Center, Texas A&M University System, Weslaco, TX 78596, USA
| | - Raviraj M. Kalunke
- Donald Danforth Plant Science Center, 975 N Warson Rd, 7 Olivette, St. Louis, MO 63132, USA
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Norero NS, Rey Burusco MF, D’Ippólito S, Décima Oneto CA, Massa GA, Castellote MA, Feingold SE, Guevara MG. Genome-Wide Analyses of Aspartic Proteases on Potato Genome ( Solanum tuberosum): Generating New Tools to Improve the Resistance of Plants to Abiotic Stress. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11040544. [PMID: 35214878 PMCID: PMC8875628 DOI: 10.3390/plants11040544] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/04/2021] [Accepted: 01/06/2022] [Indexed: 05/11/2023]
Abstract
Aspartic proteases are proteolytic enzymes widely distributed in living organisms and viruses. Although they have been extensively studied in many plant species, they are poorly described in potatoes. The present study aimed to identify and characterize S. tuberosum aspartic proteases. Gene structure, chromosome and protein domain organization, phylogeny, and subcellular predicted localization were analyzed and integrated with RNAseq data from different tissues, organs, and conditions focused on abiotic stress. Sixty-two aspartic protease genes were retrieved from the potato genome, distributed in 12 chromosomes. A high number of intronless genes and segmental and tandem duplications were detected. Phylogenetic analysis revealed eight StAP groups, named from StAPI to StAPVIII, that were differentiated into typical (StAPI), nucellin-like (StAPIIIa), and atypical aspartic proteases (StAPII, StAPIIIb to StAPVIII). RNAseq data analyses showed that gene expression was consistent with the presence of cis-acting regulatory elements on StAP promoter regions related to water deficit. The study presents the first identification and characterization of 62 aspartic protease genes and proteins on the potato genome and provides the baseline material for functional gene determinations and potato breeding programs, including gene editing mediated by CRISPR.
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Affiliation(s)
- Natalia Sigrid Norero
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - María Florencia Rey Burusco
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
- Faculty of Agricultural Sciences, University National of Mar del Plata, Balcarce B7620, Argentina
| | - Sebastián D’Ippólito
- Institute of Biological Research, University of Mar del Plata (IIB-UNMdP), Mar del Plata B7600, Argentina;
- National Scientific and Technical Research Council, Argentina (CONICET), Buenos Aires C1499, Argentina
| | - Cecilia Andrea Décima Oneto
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - Gabriela Alejandra Massa
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
- Faculty of Agricultural Sciences, University National of Mar del Plata, Balcarce B7620, Argentina
| | - Martín Alfredo Castellote
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - Sergio Enrique Feingold
- Laboratory of Agrobiotechnology IPADS (INTA—CONICET), Balcarce B7620, Argentina; (N.S.N.); (M.F.R.B.); (C.A.D.O.); (G.A.M.); (M.A.C.); (S.E.F.)
| | - María Gabriela Guevara
- Institute of Biological Research, University of Mar del Plata (IIB-UNMdP), Mar del Plata B7600, Argentina;
- National Scientific and Technical Research Council, Argentina (CONICET), Buenos Aires C1499, Argentina
- Correspondence: or
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Bekalu ZE, Dionisio G, Madsen CK, Etzerodt T, Fomsgaard IS, Brinch-Pedersen H. Barley Nepenthesin-Like Aspartic Protease HvNEP-1 Degrades Fusarium Phytase, Impairs Toxin Production, and Suppresses the Fungal Growth. FRONTIERS IN PLANT SCIENCE 2021; 12:702557. [PMID: 34394154 PMCID: PMC8358834 DOI: 10.3389/fpls.2021.702557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Nepenthesins are categorized under the subfamily of the nepenthesin-like plant aspartic proteases (PAPs) that form a distinct group of atypical PAPs. This study describes the effect of nepenthesin 1 (HvNEP-1) protease from barley (Hordeum vulgare L.) on fungal histidine acid phosphatase (HAP) phytase activity. Signal peptide lacking HvNEP-1 was expressed in Pichia pastoris and biochemically characterized. Recombinant HvNEP-1 (rHvNEP-1) strongly inhibited the activity of Aspergillus and Fusarium phytases, which are enzymes that release inorganic phosphorous from phytic acid. Moreover, rHvNEP-1 suppressed in vitro fungal growth and strongly reduced the production of mycotoxin, 15-acetyldeoxynivalenol (15-ADON), from Fusarium graminearum. The quantitative PCR analysis of trichothecene biosynthesis genes (TRI) confirmed that rHvNEP-1 strongly repressed the expression of TRI4, TRI5, TRI6, and TRI12 in F. graminearum. The co-incubation of rHvNEP-1 with recombinant F. graminearum (rFgPHY1) and Fusarium culmorum (FcPHY1) phytases induced substantial degradation of both Fusarium phytases, indicating that HvNEP-1-mediated proteolysis of the fungal phytases contributes to the HvNEP-1-based suppression of Fusarium.
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Liu Y, Han N, Wang S, Chen C, Lu J, Riaz MW, Si H, Sun G, Ma C. Genome-Wide Identification of Triticum aestivum Xylanase Inhibitor Gene Family and Inhibitory Effects of XI-2 Subfamily Proteins on Fusarium graminearum GH11 Xylanase. FRONTIERS IN PLANT SCIENCE 2021; 12:665501. [PMID: 34381472 PMCID: PMC8350787 DOI: 10.3389/fpls.2021.665501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/21/2021] [Indexed: 06/13/2023]
Abstract
Triticum aestivum xylanase inhibitor (TaXI) gene plays an important role in plant defense. Recently, TaXI-III inhibitor has been shown to play a dual role in wheat resistance to Fusarium graminearum infection. Thus, identifying the members of the TaXI gene family and clarifying its role in wheat resistance to stresses are essential for wheat resistance breeding. However, to date, no comprehensive research on TaXIs in wheat (Triticum aestivum L.) has been conducted. In this study, a total of 277 TaXI genes, including six genes that we cloned, were identified from the recently released wheat genome database (IWGSC RefSeq v1.1), which were unevenly located on 21 chromosomes of wheat. Phylogenetic analysis divided these genes into six subfamilies, all the six genes we cloned belonged to XI-2 subfamily. The exon/intron structure of most TaXI genes and the conserved motifs of proteins in the same subfamily are similar. The TaXI gene family contains 92 homologous gene pairs or clusters, 63 and 193 genes were identified as tandem replication and segmentally duplicated genes, respectively. Analysis of the cis-acting elements in the promoter of TaXI genes showed that they are involved in wheat growth, hormone-mediated signal transduction, and response to biotic and abiotic stresses. RNA-seq data analysis revealed that TaXI genes exhibited expression preference or specificity in different organs and developmental stages, as well as in diverse stress responses, which can be regulated or induced by a variety of plant hormones and stresses. In addition, the qRT-PCR data and heterologous expression analysis of six TaXI genes revealed that the genes of XI-2 subfamily have double inhibitory effect on GH11 xylanase of F. graminearum, suggesting their potential important roles in wheat resistance to F. graminearum infection. The outcomes of this study not only enhance our understanding of the TaXI gene family in wheat, but also help us to screen more candidate genes for further exploring resistance mechanism in wheat.
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Affiliation(s)
- Yang Liu
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Nannan Han
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Sheng Wang
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Can Chen
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Jie Lu
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Muhammad Waheed Riaz
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Hongqi Si
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
| | - Genlou Sun
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Biology Department, Saint Mary’s University, Halifax, NS, Canada
| | - Chuanxi Ma
- College of Agronomy, Anhui Agricultural University, Hefei, China
- Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow and Huai River Valley, Ministry of Agriculture and Rural Affairs, Hefei, China
- National United Engineering Laboratory for Crop Stress Resistance Breeding, Hefei, China
- Anhui Key Laboratory of Crop Biology, Hefei, China
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Bekalu ZE, Dionisio G, Brinch-Pedersen H. Molecular Properties and New Potentials of Plant Nepenthesins. PLANTS (BASEL, SWITZERLAND) 2020; 9:E570. [PMID: 32365700 PMCID: PMC7284499 DOI: 10.3390/plants9050570] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 04/27/2020] [Accepted: 04/28/2020] [Indexed: 12/20/2022]
Abstract
Nepenthesins are aspartic proteases (APs) categorized under the A1B subfamily. Due to nepenthesin-specific sequence features, the A1B subfamily is also named nepenthesin-type aspartic proteases (NEPs). Nepenthesins are mostly known from the pitcher fluid of the carnivorous plant Nepenthes, where they are availed for the hydrolyzation of insect protein required for the assimilation of insect nitrogen resources. However, nepenthesins are widely distributed within the plant kingdom and play significant roles in plant species other than Nepenthes. Although they have received limited attention when compared to other members of the subfamily, current data indicates that they have exceptional molecular and biochemical properties and new potentials as fungal-resistance genes. In the current review, we provide insights into the current knowledge on the molecular and biochemical properties of plant nepenthesins and highlights that future focus on them may have strong potentials for industrial applications and crop trait improvement.
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Affiliation(s)
- Zelalem Eshetu Bekalu
- Department of Agroecology, Research Center Flakkebjerg, Aarhus University, DK-4200 Slagelse, Denmark; (G.D.); (H.B.-P.)
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Fabre F, Rocher F, Alouane T, Langin T, Bonhomme L. Searching for FHB Resistances in Bread Wheat: Susceptibility at the Crossroad. FRONTIERS IN PLANT SCIENCE 2020; 11:731. [PMID: 32595664 PMCID: PMC7300258 DOI: 10.3389/fpls.2020.00731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/07/2020] [Indexed: 05/09/2023]
Abstract
Fusarium head blight (FHB), primarily caused by Fusarium graminearum, is one of the most devastating fungal wheat diseases. During the past decades, many efforts have been deployed to dissect FHB resistance, investigating both the wheat responses to infection and, more recently, the fungal determinants of pathogenicity. Although no total resistance has been identified so far, they demonstrated that some plant functions and the expression of specific genes are needed to promote FHB. Associated with the increasing list of F. graminearum effectors able to divert plant molecular processes, this fact strongly argues for a functional link between susceptibility-related factors and the fate of this disease in wheat. In this review, we gather more recent data concerning the involvement of plant and fungal genes and the functions and mechanisms in the development of FHB susceptibility, and we discuss the possibility to use them to diversify the current sources of FHB resistance.
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Rubio MB, Martínez de Alba AE, Nicolás C, Monte E, Hermosa R. Early Root Transcriptomic Changes in Wheat Seedlings Colonized by Trichoderma harzianum Under Different Inorganic Nitrogen Supplies. Front Microbiol 2019; 10:2444. [PMID: 31749777 PMCID: PMC6842963 DOI: 10.3389/fmicb.2019.02444] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/10/2019] [Indexed: 12/02/2022] Open
Abstract
Wheat is one of the most important crops worldwide. The use of plant growth promoting microorganisms, such as those of the genus Trichoderma, constitutes an alternative to chemical fertilizers, since they are cheaper and are not detrimental to the environment. However, the interaction between Trichoderma and wheat plants has been scarcely studied, at least at a molecular level. In the present work, a microarray approach was used to study the early transcriptomic changes induced in wheat roots by Trichoderma harzianum, applied alone or in combination with different concentrations of calcium nitrate [Ca(NO3)2], which was last used as nitrogen (N) source. Our results show that T. harzianum causes larger transcriptomic changes than Ca(NO3)2 in wheat roots, and such changes are different when plants are challenged with Trichoderma alone or treated with a combination of T. harzianum and Ca(NO3)2. Overall, T. harzianum activates the expression of defense-related genes at early stages of the interaction with the roots, while this fungus reduces the expression of genes related to plant growth and development. Moreover, the current study in wheat roots, subjected to the different T. harzianum and Ca(NO3)2 combinations, reveals that the number of transcriptomic changes was higher when compared against those caused by the different Ca(NO3)2 concentrations than when it was compared against those caused by T. harzianum. N metabolism gene expression changes were in agreement with the levels of nitrate reductase activity measured in plants from Trichoderma plus Ca(NO3)2 conditions. Results were also concordant with plant phenotypes, which showed reduced growth at early interaction stages when inoculated with T. harzianum or with its combination with Ca(NO3)2 at the lowest dosage. These results were in a good agreement with the recognized role of Trichoderma as an inducer of plant defense.
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Affiliation(s)
- M Belén Rubio
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - A Emilio Martínez de Alba
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Carlos Nicolás
- Department of Botany and Plant Pathology, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Enrique Monte
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
| | - Rosa Hermosa
- Department of Microbiology and Genetics, Spanish-Portuguese Institute for Agricultural Research (CIALE), University of Salamanca, Salamanca, Spain
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Wang E, Weng G, Sun H, Du H, Zhu F, Chen F, Wang Z, Hou T. Assessing the performance of the MM/PBSA and MM/GBSA methods. 10. Impacts of enhanced sampling and variable dielectric model on protein-protein Interactions. Phys Chem Chem Phys 2019; 21:18958-18969. [PMID: 31453590 DOI: 10.1039/c9cp04096j] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Enhanced sampling has been extensively used to capture the conformational transitions in protein folding, but it attracts much less attention in the studies of protein-protein recognition. In this study, we evaluated the impact of enhanced sampling methods and solute dielectric constants on the overall accuracy of the molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) and molecular mechanics/generalized Born surface area (MM/GBSA) approaches for the protein-protein binding free energy calculations. Here, two widely used enhanced sampling methods, including aMD and GaMD, and conventional molecular dynamics (cMD) simulations with two AMBER force fields (ff03 and ff14SB) were used to sample the conformations for 21 protein-protein complexes. The MM/PBSA and MM/GBSA calculation results illustrate that the standard MM/GBSA based on the cMD simulations yields the best Pearson correlation (rp = -0.523) between the predicted binding affinities and the experimental data, which is much higher than that given by MM/PBSA (rp = -0.212). Two enhanced sampling methods (aMD and GaMD) are indeed more efficient for conformational sampling, but they did not improve the binding affinity predictions for protein-protein systems, suggesting that the aMD or GaMD sampling (at least in short timescale simulations) may not be a good choice for the MM/PBSA and MM/GBSA predictions of protein-protein complexes. The solute dielectric constant of 1.0 is recommended to MM/GBSA, but a higher solute dielectric constant is recommended to MM/PBSA, especially for the systems with higher polarity on the protein-protein binding interfaces. Then, a preliminary assessment of the MM/GBSA calculations based on a variable dielectric generalized Born (VDGB) model was conducted. The results highlight the potential power of VDGB in the free energy predictions for protein-protein systems, but more thorough studies should be done in the future.
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Affiliation(s)
- Ercheng Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Gaoqi Weng
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Huiyong Sun
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Hongyan Du
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Feng Zhu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Fu Chen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Zhe Wang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China. and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
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12
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Chen F, Liu H, Sun H, Pan P, Li Y, Li D, Hou T. Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein-protein binding free energies and re-rank binding poses generated by protein-protein docking. Phys Chem Chem Phys 2018; 18:22129-39. [PMID: 27444142 DOI: 10.1039/c6cp03670h] [Citation(s) in RCA: 309] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Understanding protein-protein interactions (PPIs) is quite important to elucidate crucial biological processes and even design compounds that interfere with PPIs with pharmaceutical significance. Protein-protein docking can afford the atomic structural details of protein-protein complexes, but the accurate prediction of the three-dimensional structures for protein-protein systems is still notoriously difficult due in part to the lack of an ideal scoring function for protein-protein docking. Compared with most scoring functions used in protein-protein docking, the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) and Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) methodologies are more theoretically rigorous, but their overall performance for the predictions of binding affinities and binding poses for protein-protein systems has not been systematically evaluated. In this study, we first evaluated the performance of MM/PBSA and MM/GBSA to predict the binding affinities for 46 protein-protein complexes. On the whole, different force fields, solvation models, and interior dielectric constants have obvious impacts on the prediction accuracy of MM/GBSA and MM/PBSA. The MM/GBSA calculations based on the ff02 force field, the GB model developed by Onufriev et al. and a low interior dielectric constant (εin = 1) yield the best correlation between the predicted binding affinities and the experimental data (rp = -0.647), which is better than MM/PBSA (rp = -0.523) and a number of empirical scoring functions used in protein-protein docking (rp = -0.141 to -0.529). Then, we examined the capability of MM/GBSA to identify the possible near-native binding structures from the decoys generated by ZDOCK for 43 protein-protein systems. The results illustrate that the MM/GBSA rescoring has better capability to distinguish the correct binding structures from the decoys than the ZDOCK scoring. Besides, the optimal interior dielectric constant of MM/GBSA for re-ranking docking poses may be determined by analyzing the characteristics of protein-protein binding interfaces. Considering the relatively high prediction accuracy and low computational cost, MM/GBSA may be a good choice for predicting the binding affinities and identifying correct binding structures for protein-protein systems.
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Affiliation(s)
- Fu Chen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Peichen Pan
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China. and State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, P. R. China
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13
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Lara-Márquez A, Oyama K, Zavala-Páramo MG, Villa-Rivera MG, Conejo-Saucedo U, Cano-Camacho H. Evolutionary Analysis of Pectin Lyases of the Genus Colletotrichum. J Mol Evol 2017; 85:120-136. [PMID: 29071357 DOI: 10.1007/s00239-017-9812-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/11/2017] [Indexed: 10/18/2022]
Abstract
Pectin lyases (PNLs) are important enzymes that are involved in plant cell wall degradation during the infection process. Colletotrichum is a diverse genus of fungi, which allows the study of the evolution of PNLs and their possible role in pathogen-host interactions and lifestyle adaptations. The phylogenetic reconstruction of PNLs from Colletotrichum and analysis of selection pressures showed the formation of protein lineages by groups of species with different selection pressures and specific patterns. The analysis of positive selection at individual sites using different methods allowed for the identification of three codons with evidence of positive selection in the oligosaccharide-binding region and two codons on the antiparallel sheet, which may influence the interaction with the substrate. Seven codons on the surface of the protein, mainly in the peripheral helices of the PNLs, could have an important function in evasion of plant defenses, as has been proposed in other enzymes. According to our results, it is possible that events of genetic duplication occurred in ancestral lines, followed by episodes of genetic diversification and gene loss, probably influenced by differences in the composition of the host cell wall. Additionally, different patterns of evolution in Colletotrichum appear to be molded by a strong purifying selection and positive selection episodes that forged the observed evolutionary patterns, possibly influenced by host interaction or substrate specificity. This work represents a starting point for the study of sites that may be important for evasion of plant defenses and biotechnological purposes.
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Affiliation(s)
- Alicia Lara-Márquez
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, México
| | - Ken Oyama
- Escuela Nacional de Estudios Superiores (ENES) Unidad Morelia, Universidad Nacional Autónoma de México (UNAM), Morelia, Michoacán, México
| | - María G Zavala-Páramo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Maria G Villa-Rivera
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Ulises Conejo-Saucedo
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México
| | - Horacio Cano-Camacho
- Centro Multidisciplinario de Estudios en Biotecnología, FMVZ, Universidad Michoacana de San Nicolás de Hidalgo, Morelia, Michoacán, México.
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14
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Grisolia MJ, Peralta DA, Valdez HA, Barchiesi J, Gomez-Casati DF, Busi MV. The targeting of starch binding domains from starch synthase III to the cell wall alters cell wall composition and properties. PLANT MOLECULAR BIOLOGY 2017; 93:121-135. [PMID: 27770231 DOI: 10.1007/s11103-016-0551-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 10/13/2016] [Indexed: 05/11/2023]
Abstract
Starch binding domains of starch synthase III from Arabidopsis thaliana (SBD123) binds preferentially to cell wall polysaccharides rather than to starch in vitro. Transgenic plants overexpressing SBD123 in the cell wall are larger than wild type. Cell wall components are altered in transgenic plants. Transgenic plants are more susceptible to digestion than wild type and present higher released glucose content. Our results suggest that the transgenic plants have an advantage for the production of bioethanol in terms of saccharification of essential substrates. The plant cell wall, which represents a major source of biomass for biofuel production, is composed of cellulose, hemicelluloses, pectins and lignin. A potential biotechnological target for improving the production of biofuels is the modification of plant cell walls. This modification is achieved via several strategies, including, among others, altering biosynthetic pathways and modifying the associations and structures of various cell wall components. In this study, we modified the cell wall of A. thaliana by targeting the starch-binding domains of A. thaliana starch synthase III to this structure. The resulting transgenic plants (E8-SDB123) showed an increased biomass, higher levels of both fermentable sugars and hydrolyzed cellulose and altered cell wall properties such as higher laxity and degradability, which are valuable characteristics for the second-generation biofuels industry. The increased biomass and degradability phenotype of E8-SBD123 plants could be explained by the putative cell-wall loosening effect of the in tandem starch binding domains. Based on these results, our approach represents a promising biotechnological tool for reducing of biomass recalcitrance and therefore, the need for pretreatments.
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Affiliation(s)
- Mauricio J Grisolia
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas (CEFOBI - CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego A Peralta
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas (CEFOBI - CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Hugo A Valdez
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martin, Chascomús, Buenos Aires, Argentina
- Centro de Investigación y Desarrollo en Fermentaciones Industriales (CINDEFI), 50 y 115, 1900, La Plata, Buenos Aires, Argentina
| | - Julieta Barchiesi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas (CEFOBI - CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
| | - Diego F Gomez-Casati
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas (CEFOBI - CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martin, Chascomús, Buenos Aires, Argentina
| | - María V Busi
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas (CEFOBI - CONICET), Universidad Nacional de Rosario, Rosario, Santa Fe, Argentina.
- Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico de Chascomús (IIB-INTECH), Universidad Nacional de San Martin, Chascomús, Buenos Aires, Argentina.
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15
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Scarafoni A, Consonni A, Pessina S, Balzaretti S, Capraro J, Galanti E, Duranti M. Structural basis of the lack of endo-glucanase inhibitory activity of Lupinus albus γ-conglutin. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 99:79-85. [PMID: 26741537 DOI: 10.1016/j.plaphy.2015.11.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 10/30/2015] [Accepted: 11/16/2015] [Indexed: 06/05/2023]
Abstract
Lupin γ-conglutin and soybean BG7S are two legume seed proteins strongly similar to plant endo-β-glucanases inhibitors acting against fungal GH11 and GH12 glycoside hydrolase. However these proteins lack inhibitory activity. Here we describe the conversion of lupin γ-conglutin to an active inhibitor of endo-β-glucanases belonging to GH11 family. A set of γ-conglutin mutants was designed and expressed in Pichia pastoris, along with the wild-type protein. Unexpectedly, this latter was able to inhibit a GH11 enzyme, but not GH12, whereas the mutants were able to modulate the inhibition capacity. In lupin, γ-conglutin is naturally cleaved in two subunits, whereas in P. pastoris it is not. The lack of proteolytic cleavage is one of the reasons at the basis of the inhibitory activity of recombinant γ-conglutin. The results provide new insights about structural features at the basis of the lack of inhibitory activity of wild-type γ-conglutin and its legume homologues.
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Affiliation(s)
- Alessio Scarafoni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy.
| | - Alessandro Consonni
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Stefano Pessina
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Silvia Balzaretti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Jessica Capraro
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Elisabetta Galanti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
| | - Marcello Duranti
- Department of Food, Environmental and Nutritional Sciences (DeFENS), Università degli Studi di Milano, Milano, Italy
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16
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Zafar A, Aftab MN, Din ZU, Aftab S, Iqbal I, Shahid A, Tahir A, Haq IU. Cloning, Expression, and Purification of Xylanase Gene from Bacillus licheniformis for Use in Saccharification of Plant Biomass. Appl Biochem Biotechnol 2015; 178:294-311. [DOI: 10.1007/s12010-015-1872-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 09/24/2015] [Indexed: 11/24/2022]
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17
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Sudha G, Singh P, Swapna LS, Srinivasan N. Weak conservation of structural features in the interfaces of homologous transient protein-protein complexes. Protein Sci 2015; 24:1856-73. [PMID: 26311309 DOI: 10.1002/pro.2792] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 08/13/2015] [Accepted: 08/17/2015] [Indexed: 12/21/2022]
Abstract
Residue types at the interface of protein-protein complexes (PPCs) are known to be reasonably well conserved. However, we show, using a dataset of known 3-D structures of homologous transient PPCs, that the 3-D location of interfacial residues and their interaction patterns are only moderately and poorly conserved, respectively. Another surprising observation is that a residue at the interface that is conserved is not necessarily in the interface in the homolog. Such differences in homologous complexes are manifested by substitution of the residues that are spatially proximal to the conserved residue and structural differences at the interfaces as well as differences in spatial orientations of the interacting proteins. Conservation of interface location and the interaction pattern at the core of the interfaces is higher than at the periphery of the interface patch. Extents of variability of various structural features reported here for homologous transient PPCs are higher than the variation in homologous permanent homomers. Our findings suggest that straightforward extrapolation of interfacial nature and inter-residue interaction patterns from template to target could lead to serious errors in the modeled complex structure. Understanding the evolution of interfaces provides insights to improve comparative modeling of PPC structures.
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Affiliation(s)
- Govindarajan Sudha
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Prashant Singh
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
| | - Lakshmipuram S Swapna
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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18
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Moscetti I, Faoro F, Moro S, Sabbadin D, Sella L, Favaron F, D'Ovidio R. The xylanase inhibitor TAXI-III counteracts the necrotic activity of a Fusarium graminearum xylanase in vitro and in durum wheat transgenic plants. MOLECULAR PLANT PATHOLOGY 2015; 16:583-92. [PMID: 25346411 PMCID: PMC6638430 DOI: 10.1111/mpp.12215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The xylanase inhibitor TAXI-III has been proven to delay Fusarium head blight (FHB) symptoms caused by Fusarium graminearum in transgenic durum wheat plants. To elucidate the molecular mechanism underlying the capacity of the TAXI-III transgenic plants to limit FHB symptoms, we treated wheat tissues with the xylanase FGSG_03624, hitherto shown to induce cell death and hydrogen peroxide accumulation. Experiments performed on lemmas of flowering wheat spikes and wheat cell suspension cultures demonstrated that pre-incubation of xylanase FGSG_03624 with TAXI-III significantly decreased cell death. Most interestingly, a reduced cell death relative to control non-transgenic plants was also obtained by treating, with the same xylanase, lemmas of TAXI-III transgenic plants. Molecular modelling studies predicted an interaction between the TAXI-III residue H395 and residues E122 and E214 belonging to the active site of xylanase FGSG_03624. These results provide, for the first time, clear indications in vitro and in planta that a xylanase inhibitor can prevent the necrotic activity of a xylanase, and suggest that the reduced FHB symptoms on transgenic TAXI-III plants may be a result not only of the direct inhibition of xylanase activity secreted by the pathogen, but also of the capacity of TAXI-III to avoid host cell death.
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Affiliation(s)
- Ilaria Moscetti
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia (DAFNE), Università della Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
| | - Franco Faoro
- Dipartimento di Scienze Agrarie e Ambientali, Università degli Studi di Milano, Via Celoria 2, 20133, Milano, Italy
| | - Stefano Moro
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Davide Sabbadin
- Dipartimento di Scienze del Farmaco, Università degli Studi di Padova, Via Marzolo 5, 35131, Padova, Italy
| | - Luca Sella
- Dipartimento del Territorio e Sistemi Agro-Forestali, Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro (PD), Padova, Italy
| | - Francesco Favaron
- Dipartimento del Territorio e Sistemi Agro-Forestali, Università degli Studi di Padova, Viale dell'Università 16, 35020 Legnaro (PD), Padova, Italy
| | - Renato D'Ovidio
- Dipartimento di Scienze e Tecnologie per l'Agricoltura, le Foreste, la Natura e l'Energia (DAFNE), Università della Tuscia, Via S. Camillo de Lellis snc, 01100, Viterbo, Italy
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19
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Protein-protein docking with dynamic residue protonation states. PLoS Comput Biol 2014; 10:e1004018. [PMID: 25501663 PMCID: PMC4263365 DOI: 10.1371/journal.pcbi.1004018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 11/02/2014] [Indexed: 12/19/2022] Open
Abstract
Protein-protein interactions depend on a host of environmental factors. Local pH conditions influence the interactions through the protonation states of the ionizable residues that can change upon binding. In this work, we present a pH-sensitive docking approach, pHDock, that can sample side-chain protonation states of five ionizable residues (Asp, Glu, His, Tyr, Lys) on-the-fly during the docking simulation. pHDock produces successful local docking funnels in approximately half (79/161) the protein complexes, including 19 cases where standard RosettaDock fails. pHDock also performs better than the two control cases comprising docking at pH 7.0 or using fixed, predetermined protonation states. On average, the top-ranked pHDock structures have lower interface RMSDs and recover more native interface residue-residue contacts and hydrogen bonds compared to RosettaDock. Addition of backbone flexibility using a computationally-generated conformational ensemble further improves native contact and hydrogen bond recovery in the top-ranked structures. Although pHDock is designed to improve docking, it also successfully predicts a large pH-dependent binding affinity change in the Fc–FcRn complex, suggesting that it can be exploited to improve affinity predictions. The approaches in the study contribute to the goal of structural simulations of whole-cell protein-protein interactions including all the environmental factors, and they can be further expanded for pH-sensitive protein design. Protein-protein interactions are fundamental for biological function and are strongly influenced by their local environment. Cellular pH is tightly controlled and is one of the critical environmental factors that regulates protein-protein interactions. Three-dimensional structures of the protein complexes can help us understand the mechanism of the interactions. Since experimental determination of the structures of protein-protein complexes is expensive and time-consuming, computational docking algorithms are helpful to predict the structures. However, none of the current protein-protein docking algorithms account for the critical environmental pH effects. So we developed a pH-sensitive docking algorithm that can dynamically pick the favorable protonation states of the ionizable amino-acid residues. Compared to our previous standard docking algorithm, the new algorithm improves docking accuracy and generates higher-quality predictions over a large dataset of protein-protein complexes. We also use a case study to demonstrate efficacy of the algorithm in predicting a large pH-dependent binding affinity change that cannot be captured by the other methods that neglect pH effects. In principle, the approaches in the study can be used for rational design of pH-dependent protein inhibitors or industrial enzymes that are active over a wide range of pH values.
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Hu Q, Jin Y, Shi H, Yang W. GmFLD, a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D, promotes flowering in Arabidopsis thaliana. BMC PLANT BIOLOGY 2014; 14:263. [PMID: 25287450 PMCID: PMC4190295 DOI: 10.1186/s12870-014-0263-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 09/25/2014] [Indexed: 05/03/2023]
Abstract
BACKGROUND Flowering at an appropriate time is crucial for seed maturity and reproductive success in all flowering plants. Soybean (Glycine max) is a typical short day plant, and both photoperiod and autonomous pathway genes exist in soybean genome. However, little is known about the functions of soybean autonomous pathway genes. In this article, we examined the functions of a soybean homolog of the autonomous pathway gene FLOWERING LOCUS D (FLD), GmFLD in the flowering transition of A. thaliana. RESULTS In soybean, GmFLD is highly expressed in expanded cotyledons of seedlings, roots, and young pods. However, the expression levels are low in leaves and shoot apexes. Expression of GmFLD in A. thaliana (Col) resulted in early flowering of the transgenic plants, and rescued the late flowering phenotype of the A. thaliana fld mutant. In GmFLD transgenic plants (Col or fld background), the FLC (FLOWERING LOCUS C) transcript levels decreased whereas the floral integrators, FT and SOC1, were up-regulated when compared with the corresponding non-transgenic genotypes. Furthermore, chromatin immuno-precipitation analysis showed that in the transgenic rescued lines (fld background), the levels of both tri-methylation of histone H3 Lys-4 and acetylation of H4 decreased significantly around the transcriptional start site of FLC. This is consistent with the function of GmFLD as a histone demethylase. CONCLUSIONS Our results suggest that GmFLD is a functional ortholog of the Arabidopsis FLD and may play an important role in the regulation of chromatin state in soybean. The present data provides the first evidence for the evolutionary conservation of the components in the autonomous pathway in soybean.
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Affiliation(s)
- Qin Hu
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
| | - Ye Jin
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
| | - Huazhong Shi
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
- />Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX 79409 USA
| | - Wannian Yang
- />Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079 People’s Republic of China
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21
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Guyon K, Balagué C, Roby D, Raffaele S. Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum. BMC Genomics 2014; 15:336. [PMID: 24886033 PMCID: PMC4039746 DOI: 10.1186/1471-2164-15-336] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 04/27/2014] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The white mold fungus Sclerotinia sclerotiorum is a devastating necrotrophic plant pathogen with a remarkably broad host range. The interaction of necrotrophs with their hosts is more complex than initially thought, and still poorly understood. RESULTS We combined bioinformatics approaches to determine the repertoire of S. sclerotiorum effector candidates and conducted detailed sequence and expression analyses on selected candidates. We identified 486 S. sclerotiorum secreted protein genes expressed in planta, many of which have no predicted enzymatic activity and may be involved in the interaction between the fungus and its hosts. We focused on those showing (i) protein domains and motifs found in known fungal effectors, (ii) signatures of positive selection, (iii) recent gene duplication, or (iv) being S. sclerotiorum-specific. We identified 78 effector candidates based on these properties. We analyzed the expression pattern of 16 representative effector candidate genes on four host plants and revealed diverse expression patterns. CONCLUSIONS These results reveal diverse predicted functions and expression patterns in the repertoire of S. sclerotiorum effector candidates. They will facilitate the functional analysis of fungal pathogenicity determinants and should prove useful in the search for plant quantitative disease resistance components active against the white mold.
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Affiliation(s)
| | | | | | - Sylvain Raffaele
- INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, F-31326, Castanet-Tolosan, France.
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22
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Paës G, Berrin JG, Beaugrand J. GH11 xylanases: Structure/function/properties relationships and applications. Biotechnol Adv 2011; 30:564-92. [PMID: 22067746 DOI: 10.1016/j.biotechadv.2011.10.003] [Citation(s) in RCA: 281] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2011] [Revised: 10/06/2011] [Accepted: 10/13/2011] [Indexed: 01/02/2023]
Abstract
For technical, environmental and economical reasons, industrial demands for process-fitted enzymes have evolved drastically in the last decade. Therefore, continuous efforts are made in order to get insights into enzyme structure/function relationships to create improved biocatalysts. Xylanases are hemicellulolytic enzymes, which are responsible for the degradation of the heteroxylans constituting the lignocellulosic plant cell wall. Due to their variety, xylanases have been classified in glycoside hydrolase families GH5, GH8, GH10, GH11, GH30 and GH43 in the CAZy database. In this review, we focus on GH11 family, which is one of the best characterized GH families with bacterial and fungal members considered as true xylanases compared to the other families because of their high substrate specificity. Based on an exhaustive analysis of the sequences and 3D structures available so far, in relation with biochemical properties, we assess biochemical aspects of GH11 xylanases: structure, catalytic machinery, focus on their "thumb" loop of major importance in catalytic efficiency and substrate selectivity, inhibition, stability to pH and temperature. GH11 xylanases have for a long time been used as biotechnological tools in various industrial applications and represent in addition promising candidates for future other uses.
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Affiliation(s)
- Gabriel Paës
- INRA, UMR614 FARE, 2 esplanade Roland-Garros, F-51686 Reims, France.
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Yoshizawa T, Shimizu T, Yamabe M, Taichi M, Nishiuchi Y, Shichijo N, Unzai S, Hirano H, Sato M, Hashimoto H. Crystal structure of basic 7S globulin, a xyloglucan-specific endo-β-1,4-glucanase inhibitor protein-like protein from soybean lacking inhibitory activity against endo-β-glucanase. FEBS J 2011; 278:1944-54. [PMID: 21457461 DOI: 10.1111/j.1742-4658.2011.08111.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
β-Linked glucans such as cellulose and xyloglucan are important components of the cell walls of most dicotyledonous plants. These β-linked glucans are constantly exposed to degradation by various endo-β-glucanases from pathogenic bacteria and fungi. To protect the cell wall from degradation by such enzymes, plants secrete proteinaceous endo-β-glucanases inhibitors, such as xyloglucan-specific endo-β-1,4-glucanase inhibitor protein (XEGIP) in tomato. XEGIPs typically inhibit xyloglucanase, a member of the glycoside hydrolase (GH)12 family. XEGIPs are also found in legumes, including soybean and lupin. To date, tomato XEGIP has been well studied, whereas XEGIPs from legumes are less well understood. Here, we determined the crystal structure of basic 7S globulin (Bg7S), a XEGIP from soybean, which represents the first three-dimensional structure of XEGIP. Bg7S formed a tetramer with pseudo-222 symmetry. Analytical centrifugation and size exclusion chromatography experiments revealed that the assembly of Bg7S in solution depended on pH. The structure of Bg7S was similar to that of a xylanase inhibitor protein from wheat (Tritinum aestivum xylanase inhibitor) that inhibits GH11 xylanase. Surprisingly, Bg7S lacked inhibitory activity against not only GH11 but also GH12 enzymes. In addition, we found that XEGIPs from azukibean, yardlongbean and mungbean also had no impact on the activity of either GH12 or GH11 enzymes, indicating that legume XEGIPs generally do not inhibit these enzymes. We reveal the structural basis of why legume XEGIPs lack this inhibitory activity. This study will provide significant clues for understanding the physiological role of Bg7S.
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Affiliation(s)
- Takuya Yoshizawa
- Graduate School of Nanobioscience, Yokohama City University, Japan
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Gusakov AV. Proteinaceous inhibitors of microbial xylanases. BIOCHEMISTRY (MOSCOW) 2010; 75:1185-99. [DOI: 10.1134/s0006297910100019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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