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Li J, Wang S, Chen Z, Wang Y. A Bipartite Network Module-Based Project to Predict Pathogen-Host Association. Front Genet 2020; 10:1357. [PMID: 32038713 PMCID: PMC6992693 DOI: 10.3389/fgene.2019.01357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 12/11/2019] [Indexed: 12/23/2022] Open
Abstract
Pathogen-host interactions play an important role in understanding the mechanism by which a pathogen can infect its host. Some approaches for predicting pathogen-host association have been developed, but prediction accuracy is still low. In this paper, we propose a bipartite network module-based approach to improve prediction accuracy. First, a bipartite network with pathogens and hosts is constructed. Next, pathogens and hosts are divided into different modules respectively. Then, modular information on the pathogens and hosts is added into a bipartite network projection model and the association scores between pathogens and hosts are calculated. Finally, leave-one-out cross-validation is used to estimate the performance of the proposed method. Experimental results show that the proposed method performs better in predicting pathogen-host association than other methods, and some potential pathogen-host associations with higher prediction scores are also confirmed by the results of biological experiments in the publically available literature.
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Affiliation(s)
- Jie Li
- School of Computer Science and Technology, Harbin Institute of Technology, Harbin, China
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Rocha RO, Wilson RA. Essential, deadly, enigmatic: Polyamine metabolism and roles in fungal cells. FUNGAL BIOL REV 2019. [DOI: 10.1016/j.fbr.2018.07.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Vilas JM, Romero FM, Rossi FR, Marina M, Maiale SJ, Calzadilla PI, Pieckenstain FL, Ruiz OA, Gárriz A. Modulation of plant and bacterial polyamine metabolism during the compatible interaction between tomato and Pseudomonas syringae. JOURNAL OF PLANT PHYSIOLOGY 2018; 231:281-290. [PMID: 30342327 DOI: 10.1016/j.jplph.2018.09.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 09/21/2018] [Accepted: 09/22/2018] [Indexed: 05/25/2023]
Abstract
The polyamines putrescine, spermidine and spermine participate in a variety of cellular processes in all organisms. Many studies have shown that these polycations are important for plant immunity, as well as for the virulence of diverse fungal phytopathogens. However, the polyamines' roles in the pathogenesis of phytopathogenic bacteria have not been thoroughly elucidated to date. To obtain more information on this topic, we assessed the changes in polyamine homeostasis during the infection of tomato plants by Pseudomonas syringae. Our results showed that polyamine biosynthesis and catabolism are activated in both tomato and bacteria during the pathogenic interaction. This activation results in the accumulation of putrescine in whole leaf tissues, as well as in the apoplastic fluids, which is explained by the induction of its synthesis in plant cells and also on the basis of its excretion by bacteria. We showed that the excretion of this polyamine by P. syringae is stimulated under virulence-inducing conditions, suggesting that it plays a role in plant colonization. However, no activation of bacterial virulence traits or induction of plant invasion was observed after the exogenous addition of putrescine. In addition, no connection was found between this polyamine and plant defence responses. Although further research is warranted to unravel the biological functions of these molecules during plant-bacterial interactions, this study contributes to a better understanding of the changes associated with the homeostasis of polyamines during plant pathogenesis.
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Affiliation(s)
- Juan Manuel Vilas
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Fernando Matías Romero
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Franco Rubén Rossi
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - María Marina
- Laboratorio de fisiología y bioquímica de la maduración de frutos, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Santiago Javier Maiale
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Pablo Ignacio Calzadilla
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Fernando Luis Pieckenstain
- Laboratorio de interacciones planta-microorganismo, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Oscar Adolfo Ruiz
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina
| | - Andrés Gárriz
- Laboratorio de estrés biótico y abiótico en plantas, Instituto de Investigaciones Biotecnológicas-Instituto Tecnológico de Chascomús (IIB-INTECh), Universidad Nacional de San Martín (UNSAM), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Avenida Intendente Marino Km 8.200 CC 164 (7130), Chascomús, Buenos Aires, Argentina.
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Espasandin FD, Maiale SJ, Calzadilla P, Ruiz OA, Sansberro PA. Transcriptional regulation of 9-cis-epoxycarotenoid dioxygenase (NCED) gene by putrescine accumulation positively modulates ABA synthesis and drought tolerance in Lotus tenuis plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2014; 76:29-35. [PMID: 24448322 DOI: 10.1016/j.plaphy.2013.12.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2013] [Accepted: 12/21/2013] [Indexed: 05/05/2023]
Abstract
The accumulation of putrescine (Put) and increased arginine decarboxylase (ADC, EC 4.1.1.19) activity levels in response to osmotic stress has been reported; however, the biological meaning of this increase remains unclear. To obtain new insights into these questions, we studied the drought response of a transgenic Lotus tenuis line that expresses the oat ADC gene, which is driven by the stress-inducible pRD29A promoter. This line contains high levels of Put with no changes in spermidine and spermine contents, even under water deficits. Our results indicate that the biochemical and morphological responses to dehydration correlate with the Put level and provide evidence that Put controls the ABA content in response to drought by modulating ABA biosynthesis at the transcriptional level.
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Affiliation(s)
- Fabiana D Espasandin
- Instituto de Botánica del Nordeste (IBONE-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, CC: 209, W3402BKG Corrientes, Argentina
| | - Santiago J Maiale
- Unidad de Biotecnología 1 IIB-INTECh (CONICET), CC: 164, B7130IWA Chascomús, Argentina
| | - Pablo Calzadilla
- Unidad de Biotecnología 1 IIB-INTECh (CONICET), CC: 164, B7130IWA Chascomús, Argentina
| | - Oscar A Ruiz
- Unidad de Biotecnología 1 IIB-INTECh (CONICET), CC: 164, B7130IWA Chascomús, Argentina
| | - Pedro A Sansberro
- Instituto de Botánica del Nordeste (IBONE-CONICET), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste, Sargento Cabral 2131, CC: 209, W3402BKG Corrientes, Argentina.
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Profiling the aminopropyltransferases in plants: their structure, expression and manipulation. Amino Acids 2011; 42:813-30. [PMID: 21861167 DOI: 10.1007/s00726-011-0998-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Accepted: 06/28/2011] [Indexed: 10/17/2022]
Abstract
Polyamines are organic polycations that are involved in a wide range of cellular activities related to growth, development, and stress response in plants. Higher polyamines spermidine and spermine are synthesized in plants and animals by a class of enzymes called aminopropyltransferases that transfer aminopropyl moieties (derived from decarboxylated S-adenosylmethionine) to putrescine and spermidine to produce spermidine and spermine, respectively. The higher polyamines show a much tighter homeostatic regulation of their metabolism than the diamine putrescine in most plants; therefore, the aminopropyltransferases are of high significance. We present here a comprehensive summary of the current literature on plant aminopropyltransferases including their distribution, biochemical properties, genomic organization, pattern of expression during development, and their responses to abiotic stresses, and manipulation of their cellular activity through chemical inhibitors, mutations, and genetic engineering. This minireview complements several recent reviews on the overall biosynthetic pathway of polyamines and their physiological roles in plants and animals. It is concluded that (1) plants often have two copies of the common aminopropyltransferase genes which exhibit redundancy of function, (2) their genomic organization is highly conserved, (3) direct enzyme activity data on biochemical properties of these enzymes are scant, (4) often there is a poor correlation among transcripts, enzyme activity and cellular contents of the respective polyamine, and (5) transgenic work mostly confirms the tight regulation of cellular contents of spermidine and spermine. An understanding of expression and regulation of aminopropyltransferases at the metabolic level will help us in effective use of genetic engineering approaches for the improvement in nutritional value and stress responses of plants.
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Maiale SJ, Marina M, Sánchez DH, Pieckenstain FL, Ruiz OA. In vitro and in vivo inhibition of plant polyamine oxidase activity by polyamine analogues. PHYTOCHEMISTRY 2008; 69:2552-8. [PMID: 18783804 DOI: 10.1016/j.phytochem.2008.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 05/17/2008] [Accepted: 07/16/2008] [Indexed: 05/26/2023]
Abstract
Polyamine oxidase from Avena sativa L. cv. Cristal seedlings was purified to homogeneity using a simple four-step purification protocol including an infiltration washing technique. The enzyme had a high affinity for spermidine and spermine (K(m) approximately 5.5 and 1.2 microM, respectively), and also oxidized norspermidine (K(m) approximately 64.0 microM). Natural and synthetic diamines, cyclohexylamine, the putrescine analogue 1-aminooxy-3-aminopropane, and several polyamine analogues had inhibitory effects on polyamine oxidase activity and none were substrates. No inhibitory effect was observed on spermidine oxidation when the reaction product 1,3-diaminopropane was added. By contrast, 1-aminooxy-3-aminopropane showed mixed inhibition kinetics and a K(i) value of 0.113 mM. In addition, in vitro enzymatic activity assays showed that the oligoamine [3,8,13,18,23,28,33,38,43,48-deca-aza-(trans-25)-pentacontene], the tetramine 1,14-bis-[ethylamino]-5,10-diazatetradecane, and the pentamine 1,19-bis-[ethylamino]-5,10,15-triazanonadecane, displayed potent competitive inhibitory activities against polyamine oxidase with K(i) values of 5.8, 110.0 and 7.6 nM, respectively, where cyclohexylamine was a weak competitive inhibitor with a K(i) value of 0.5 mM. These analogues did not inhibit mycelial growth of the fungus Sclerotinia sclerotiorum (Lib.) De Bary and the bacterium Pseudomonas viridiflava (Burkholder) Dowson in vitro. On the contrary, with concentrations similar to those used for polyamine analogues, guazatine (a well-known fungicide and at the same time, a polyamine oxidase inhibitor) inhibited ( approximately 85%) S. sclerotiorum mycelial growth on Czapek-Dox medium. Finally, the analogue 1,19-bis-ethylamino-5,10,15-triazanonadecane inhibited polyamine oxidase activity observed in segments of maize leaves in vivo. The results obtained provide insights into research on the influence of polyamine oxidase activity on plant biotic and abiotic stresses.
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Affiliation(s)
- Santiago J Maiale
- IIB-INTECH, Camino de Circunvalación de la Laguna km 6, Casilla de Correo 164, Provincia de Buenos Aires, B7130IWA Chascomús, Argentina
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Polyamine metabolism during sclerotial development of Sclerotinia sclerotiorum. ACTA ACUST UNITED AC 2008; 112:414-22. [DOI: 10.1016/j.mycres.2007.10.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 09/12/2007] [Accepted: 10/31/2007] [Indexed: 11/21/2022]
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Tang W, Newton RJ. Polyamines promote root elongation and growth by increasing root cell division in regenerated Virginia pine (Pinus virginiana Mill.) plantlets. PLANT CELL REPORTS 2005; 24:581-9. [PMID: 16160835 DOI: 10.1007/s00299-005-0021-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Revised: 03/05/2005] [Accepted: 06/04/2005] [Indexed: 05/04/2023]
Abstract
Polyamines have been demonstrated to play an important role in adventitious root formation and development in plants. Here, we present a detailed analysis of influence of exogenously added polyamines on adventitious root development and its relationship to cold tolerance in Virginia pine (Pinus virginia Mill.). Our results demonstrated that polyamines putrescine (Put), spermidine (Spd), and spermine (Spm) at 0.001 mM improve rooting frequency and promote root elongation. Put, Spd, and Spm at 0.01-1 mM decrease rooting frequency and reduce root elongation root elongation. Measurements of diamine oxidase (DAO, EC 1.4.3.6) and polyamine oxidase (PAO, EC 1.4.3.4) activities showed that higher DAO and PAO enzyme activities were obtained when high concentrations of polyamines were applied and when plantlets were treated for 5-7 week at 4 degrees C and 16 degrees C. Survival rate of plantlets increased with the treatment of polyamines at low temperature. Polyamines increased mitotic index of cells in root tips of regenerated plantlet cultured on medium containing 0.001 microM Put, Spd, or Spm, but did not increase mitotic index in tissues of needle tips of the same plantlets. These results demonstrated that polyamines promote root elongation and growth by increasing root cell division in regenerated Virginia pine plantlets.
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Affiliation(s)
- Wei Tang
- Department of Biology, Howell Science Complex, East Carolina University, Greenville, NC 27858-4353, USA.
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