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Xue Y, Li W, Li M, Ru N, Chen S, Jiu M, Feng H, Wei L, Daly P, Zhou D. Biological Control of a Root-Knot Nematode Meloidogyne incognita Infection of Tomato ( Solanum lycopersicum L.) by the Oomycete Biocontrol Agent Pythium oligandrum. J Fungi (Basel) 2024; 10:265. [PMID: 38667936 PMCID: PMC11051105 DOI: 10.3390/jof10040265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/13/2024] [Accepted: 03/15/2024] [Indexed: 04/28/2024] Open
Abstract
The biocontrol agent Pythium oligandrum, which is a member of the phylum Oomycota, can control diseases caused by a taxonomically wide range of plant pathogens, including fungi, bacteria, and oomycetes. However, whether P. oligandrum could control diseases caused by plant root-knot nematodes (RKNs) was unknown. We investigated a recently isolated P. oligandrum strain GAQ1, and the P. oligandrum strain CBS530.74, for the control of an RKN Meloidogyne incognita infection of tomato (Solanum lycopersicum L.). Initially, P. oligandrum culture filtrates were found to be lethal to M. incognita second-stage juveniles (J2s) with up to 84% mortality 24 h after treatment compared to 14% in the control group. Consistent with the lethality to M. incognita J2s, tomato roots treated with P. oligandrum culture filtrates reduced their attraction of nematodes, and the number of nematodes penetrating the roots was reduced by up to 78%. In a greenhouse pot trial, the P. oligandrum GAQ1 inoculation of tomato plants significantly reduced the gall number by 58% in plants infected with M. incognita. Notably, the P. oligandrum GAQ1 mycelial treatment significantly increased tomato plant height (by 36%), weight (by 27%), and root weight (by 48%). A transcriptome analysis of tomato seedling roots inoculated with the P. oligandrum GAQ1 strain identified ~2500 differentially expressed genes. The enriched GO terms and annotations in the up-regulated genes suggested a modulation of the plant hormone-signaling and defense-related pathways in response to P. oligandrum. In conclusion, our results support that P. oligandrum GAQ1 can serve as a potential biocontrol agent for M. incognita control in tomato. Multiple mechanisms appear to contribute to the biocontrol effect, including the direct inhibition of M. incognita, the potential priming of tomato plant defenses, and plant growth promotion.
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Affiliation(s)
- Yuwei Xue
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (Y.X.); (W.L.)
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
| | - Weishan Li
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (Y.X.); (W.L.)
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing 210042, China
| | - Mengnan Li
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
- College of Landscape and Ecological Engineering, Hebei University of Engineering, Handan 471023, China
| | - Ningchen Ru
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Siqiao Chen
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
- Fungal Genomics Laboratory (FungiG), Nanjing Agricultural University, Nanjing 210095, China
| | - Min Jiu
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, China; (Y.X.); (W.L.)
| | - Hui Feng
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
| | - Lihui Wei
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
- School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Paul Daly
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
| | - Dongmei Zhou
- Key Lab of Food Quality and Safety of Jiangsu Province—State Key Laboratory Breeding Base, Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (M.L.); (N.R.); (S.C.); (H.F.); (L.W.)
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Man J, Harrington TA, Lally K, Bartlett ME. Asymmetric Evolution of Protein Domains in the Leucine-Rich Repeat Receptor-Like Kinase Family of Plant Signaling Proteins. Mol Biol Evol 2023; 40:msad220. [PMID: 37787619 PMCID: PMC10588794 DOI: 10.1093/molbev/msad220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/29/2023] [Accepted: 09/26/2023] [Indexed: 10/04/2023] Open
Abstract
The coding sequences of developmental genes are expected to be deeply conserved, with cis-regulatory change driving the modulation of gene function. In contrast, proteins with roles in defense are expected to evolve rapidly, in molecular arms races with pathogens. However, some gene families include both developmental and defense genes. In these families, does the tempo and mode of evolution differ between genes with divergent functions, despite shared ancestry and structure? The leucine-rich repeat receptor-like kinase (LRR-RLKs) protein family includes members with roles in plant development and defense, thus providing an ideal system for answering this question. LRR-RLKs are receptors that traverse plasma membranes. LRR domains bind extracellular ligands; RLK domains initiate intracellular signaling cascades in response to ligand binding. In LRR-RLKs with roles in defense, LRR domains evolve faster than RLK domains. To determine whether this asymmetry extends to LRR-RLKs that function primarily in development, we assessed evolutionary rates and tested for selection acting on 11 subfamilies of LRR-RLKs, using deeply sampled protein trees. To assess functional evolution, we performed heterologous complementation assays in Arabidopsis thaliana (Arabidopsis). We found that the LRR domains of all tested LRR-RLK proteins evolved faster than their cognate RLK domains. All tested subfamilies of LRR-RLKs had strikingly similar patterns of molecular evolution, despite divergent functions. Heterologous transformation experiments revealed that multiple mechanisms likely contribute to the evolution of LRR-RLK function, including escape from adaptive conflict. Our results indicate specific and distinct evolutionary pressures acting on LRR versus RLK domains, despite diverse organismal roles for LRR-RLK proteins.
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Affiliation(s)
- Jarrett Man
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
| | - T A Harrington
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
| | - Kyra Lally
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
| | - Madelaine E Bartlett
- Department of Biology, University of Massachusetts Amherst, Amherst, MA 01002, USA
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Homma F, Huang J, van der Hoorn RAL. AlphaFold-Multimer predicts cross-kingdom interactions at the plant-pathogen interface. Nat Commun 2023; 14:6040. [PMID: 37758696 PMCID: PMC10533508 DOI: 10.1038/s41467-023-41721-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Adapted plant pathogens from various microbial kingdoms produce hundreds of unrelated small secreted proteins (SSPs) with elusive roles. Here, we used AlphaFold-Multimer (AFM) to screen 1879 SSPs of seven tomato pathogens for interacting with six defence-related hydrolases of tomato. This screen of 11,274 protein pairs identified 15 non-annotated SSPs that are predicted to obstruct the active site of chitinases and proteases with an intrinsic fold. Four SSPs were experimentally verified to be inhibitors of pathogenesis-related subtilase P69B, including extracellular protein-36 (Ecp36) and secreted-into-xylem-15 (Six15) of the fungal pathogens Cladosporium fulvum and Fusarium oxysporum, respectively. Together with a P69B inhibitor from the bacterial pathogen Xanthomonas perforans and Kazal-like inhibitors of the oomycete pathogen Phytophthora infestans, P69B emerges as an effector hub targeted by different microbial kingdoms, consistent with a diversification of P69B orthologs and paralogs. This study demonstrates the power of artificial intelligence to predict cross-kingdom interactions at the plant-pathogen interface.
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Affiliation(s)
- Felix Homma
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
| | - Jie Huang
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, OX1 3RB, Oxford, UK
| | - Renier A L van der Hoorn
- The Plant Chemetics Laboratory, Department of Biology, University of Oxford, OX1 3RB, Oxford, UK.
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Zhang B, Zhang M, Jia X, Hu G, Ren F, Fan X, Dong Y. Integrated Transcriptome and Metabolome Dissecting Interaction between Vitis vinifera L. and Grapevine Fabavirus. Int J Mol Sci 2023; 24:ijms24043247. [PMID: 36834661 PMCID: PMC9961852 DOI: 10.3390/ijms24043247] [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: 12/07/2022] [Revised: 01/22/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Grapevine fabavirus (GFabV) is a novel member of the Fabavirus genus associated with chlorotic mottling and deformation symptoms in grapevines. To gain insights into the interaction between GFabV and grapevines, V. vinifera cv. 'Summer Black' infected with GFabV was investigated under field conditions through physiological, agronomic, and multi-omics approaches. GFabV induced significant symptoms on 'Summer Black', and caused a moderate decrease in physiological efficiency. In GFabV-infected plants, alterations in carbohydrate- and photosynthesis-related genes might trigger some defense responses. In addition, secondary metabolism involved in plant defense was progressively induced by GFabV. Jasmonic acid and ethylene signaling were down-regulated in GFabV-infected leaves and berries along with the expression of proteins related to LRR and protein kinases, suggesting that GFabV can block the defense in healthy leaves and berries. Furthermore, this study provided biomarkers for early monitoring of GFabV infection in grapevines, and contributed to a better understanding of the complex grapevine-virus interaction.
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Affiliation(s)
| | | | | | | | | | - Xudong Fan
- Correspondence: (X.F.); (Y.D.); Tel.: +86-139-4292-9163 (X.F.); +86-138-9829-5984 (Y.D.)
| | - Yafeng Dong
- Correspondence: (X.F.); (Y.D.); Tel.: +86-139-4292-9163 (X.F.); +86-138-9829-5984 (Y.D.)
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A Proteinaceous Alpha-Amylase Inhibitor from Moringa Oleifera Leaf Extract: Purification, Characterization, and Insecticide Effects against C. maculates Insect Larvae. Molecules 2022; 27:molecules27134222. [PMID: 35807466 PMCID: PMC9268253 DOI: 10.3390/molecules27134222] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/15/2022] [Accepted: 06/20/2022] [Indexed: 11/26/2022] Open
Abstract
The main objective of the current study was the extraction, purification, and enzymatic characterization of a potent proteinaceous amylase inhibitor from Moringa oleifera. The antimicrobial potential and insecticide effects against C. maculates insect larvae were also studied. The α-amylase inhibitor was extracted in methanol (with an inhibitory activity of 65.6% ± 4.93). Afterwards, the inhibitor αAI.Mol was purified after a heat treatment at 70 °C for 15 min followed by one chromatographic step of Sephadex G-50. An apparent molecular weight of 25 kDa was analyzed, and the N-terminal sequence showed the highest identity level (89%) with the monomeric α-amylase inhibitor from Triticum dicoccoides. αAI.Mol was found to tolerate pH values ranging from 5.0 to 11.0 and showed maximal activity at pH 9.0. Thermal stability was remarkably important, since the inhibitory activity was maintained at 55% after 1 h of incubation at 70 °C and at 53% after an incubation of 45 min at 80 °C. The potency of the current purified inhibitor against amylases from different origins indicates that αAI.Mol seems to possess the highest affinity toward human salivary α-amylase (90% inhibitory activity), followed by the α-amylase of insects Callosobruchus maculatus and Tribolium confusum (71% and 61%, respectively). The kinetic parameters were also calculated, and the Kmax and Vmax of the digestive amylase were estimated at 185 (mmol/min/mg) and 0.13 mM, respectively. The inhibitor possesses a strong bactericidal effect against Gram+ and Gram- strains, and the MIC values were >1 against B. cereus but >6 against E. coli. Interestingly, the rates of survival and pupation of C. maculates insect larvae were remarkably affected by the purified αAI.Mol from Moringa oleifera.
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Xu J, Zhang N, Wang K, Xian Q, Dong J, Qi X, Chen X. Chitinase Chi 2 Positively Regulates Cucumber Resistance against Fusarium oxysporum f. sp. cucumerinum. Genes (Basel) 2021; 13:62. [PMID: 35052402 PMCID: PMC8775131 DOI: 10.3390/genes13010062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 11/29/2022] Open
Abstract
Cucumber (Cucumis sativus L.) is an important vegetable crop worldwide, and Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. cucumerinum (Foc), severely restricts cucumber growth and yield. Accumulating lines of evidence indicate that chitinases play important roles in attacking the invading fungal pathogens through catalyzing their cell wall degradation. Here, we identified the chitinase (Chi) genes in cucumber and further screened the FW-responsive genes via a comparative transcriptome analysis and found that six common genes were predominantly expressed in roots but also significantly upregulated after Foc infection. Expression verification further conformed that Chi2 and Chi14 were obviously induced by Foc as well as by hormone treatments, compared with the controls. The purified Chi2 and Chi14 proteins significantly affected the growth of Foc in vitro, compared with the controls. Knockdown of Chi2 in cucumber by virus-induced gene silencing (VIGS) increased susceptibility to FW, compared with the Chi14-silenced and control plants, and silencing of Chi2 drastically impaired gene activation in the jasmonic acid pathway, suggesting that the Chi2 gene might play positive roles in cucumber FW defense and, therefore, can provide a gene resource for developing cucumber-FW-resistance breeding programs.
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Affiliation(s)
- Jun Xu
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
| | - Ningyuan Zhang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
| | - Ke Wang
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
| | - Qianqian Xian
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
| | - Jingping Dong
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, Yangzhou 225009, China; (J.X.); (N.Z.); (K.W.); (Q.X.); (J.D.); (X.Q.)
- State Key Laboratory of Vegetable Germplasm Innovation, Tianjin 300192, China
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Gracz-Bernaciak J, Mazur O, Nawrot R. Functional Studies of Plant Latex as a Rich Source of Bioactive Compounds: Focus on Proteins and Alkaloids. Int J Mol Sci 2021; 22:12427. [PMID: 34830309 PMCID: PMC8620047 DOI: 10.3390/ijms222212427] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/13/2021] [Indexed: 01/03/2023] Open
Abstract
Latex, a sticky emulsion produced by specialized cells called laticifers, is a crucial part of a plant's defense system against herbivory and pathogens. It consists of a broad spectrum of active compounds, which are beneficial not only for plants, but for human health as well, enough to mention the use of morphine or codeine from poppy latex. Here, we reviewed latex's general role in plant physiology and the significance of particular compounds (alkaloids and proteins) to its defense system with the example of Chelidonium majus L. from the poppy family. We further attempt to present latex chemicals used so far in medicine and then focus on functional studies of proteins and other compounds with potential pharmacological activities using modern techniques such as CRISPR/Cas9 gene editing. Despite the centuries-old tradition of using latex-bearing plants in therapies, there are still a lot of promising molecules waiting to be explored.
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Affiliation(s)
| | | | - Robert Nawrot
- Molecular Virology Research Unit, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Poznań, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; (J.G.-B.); (O.M.)
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Carrillo MGC, Martin F, Variar M, Bhatt JC, L Perez-Quintero A, Leung H, Leach JE, Vera Cruz CM. Accumulating candidate genes for broad-spectrum resistance to rice blast in a drought-tolerant rice cultivar. Sci Rep 2021; 11:21502. [PMID: 34728643 PMCID: PMC8563964 DOI: 10.1038/s41598-021-00759-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 10/11/2021] [Indexed: 11/09/2022] Open
Abstract
Biotic stresses, including diseases, severely affect rice production, compromising producers’ ability to meet increasing global consumption. Understanding quantitative responses for resistance to diverse pathogens can guide development of reliable molecular markers, which, combined with advanced backcross populations, can accelerate the production of more resistant varieties. A candidate gene (CG) approach was used to accumulate different disease QTL from Moroberekan, a blast-resistant rice variety, into Vandana, a drought-tolerant variety. The advanced backcross progeny were evaluated for resistance to blast and tolerance to drought at five sites in India and the Philippines. Gene-based markers were designed to determine introgression of Moroberekan alleles for 11 CGs into the progeny. Six CGs, coding for chitinase, HSP90, oxalate oxidase, germin-like proteins, peroxidase and thaumatin-like protein, and 21 SSR markers were significantly associated with resistance to blast across screening sites. Multiple lines with different combinations, classes and numbers of CGs were associated with significant levels of race non-specific resistance to rice blast and sheath blight. Overall, the level of resistance effective in multiple locations was proportional to the number of CG alleles accumulated in advanced breeding lines. These disease resistant lines maintained tolerance to drought stress at the reproductive stage under blast disease pressure.
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Affiliation(s)
- Maria Gay C Carrillo
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Federico Martin
- Agricultural Biology, Colorado State University, 307 University Avenue, Fort Collins, CO, 80523-1177, USA
| | - Mukund Variar
- Central Rainfed Upland Rice Research Station, PO Box 48, Hazaribag, 825 301, India
| | - J C Bhatt
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan (VPKAS), Almora, Uttarakhand, India
| | - Alvaro L Perez-Quintero
- Agricultural Biology, Colorado State University, 307 University Avenue, Fort Collins, CO, 80523-1177, USA
| | - Hei Leung
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Jan E Leach
- Agricultural Biology, Colorado State University, 307 University Avenue, Fort Collins, CO, 80523-1177, USA.
| | - Casiana M Vera Cruz
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Adamec L, Matušíková I, Pavlovič A. Recent ecophysiological, biochemical and evolutional insights into plant carnivory. ANNALS OF BOTANY 2021; 128:241-259. [PMID: 34111238 PMCID: PMC8389183 DOI: 10.1093/aob/mcab071] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 06/07/2021] [Indexed: 05/02/2023]
Abstract
BACKGROUND Carnivorous plants are an ecological group of approx. 810 vascular species which capture and digest animal prey, absorb prey-derived nutrients and utilize them to enhance their growth and development. Extant carnivorous plants have evolved in at least ten independent lineages, and their adaptive traits represent an example of structural and functional convergence. Plant carnivory is a result of complex adaptations to mostly nutrient-poor, wet and sunny habitats when the benefits of carnivory exceed the costs. With a boost in interest and extensive research in recent years, many aspects of these adaptations have been clarified (at least partly), but many remain unknown. SCOPE We provide some of the most recent insights into substantial ecophysiological, biochemical and evolutional particulars of plant carnivory from the functional viewpoint. We focus on those processes and traits in carnivorous plants associated with their ecological characterization, mineral nutrition, cost-benefit relationships, functioning of digestive enzymes and regulation of the hunting cycle in traps. We elucidate mechanisms by which uptake of prey-derived nutrients leads to stimulation of photosynthesis and root nutrient uptake. CONCLUSIONS Utilization of prey-derived mineral (mainly N and P) and organic nutrients is highly beneficial for plants and increases the photosynthetic rate in leaves as a prerequisite for faster plant growth. Whole-genome and tandem gene duplications brought gene material for diversification into carnivorous functions and enabled recruitment of defence-related genes. Possible mechanisms for the evolution of digestive enzymes are summarized, and a comprehensive picture on the biochemistry and regulation of prey decomposition and prey-derived nutrient uptake is provided.
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Affiliation(s)
- Lubomír Adamec
- Institute of Botany of the Czech Academy of Sciences, Dukelská 135, CZ-379 01 Třeboň, Czech Republic
| | - Ildikó Matušíková
- University of Ss. Cyril and Methodius, Department of Ecochemistry and Radioecology, J. Herdu 2, SK-917 01 Trnava, Slovak Republic
| | - Andrej Pavlovič
- Department of Biophysics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic
- For correspondence. E-mail
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Application of a robust microplate assay to determine induced β-1,3-glucanase and chitinase activity in the cotton plant. Biotechniques 2021; 70:202-208. [PMID: 33512241 DOI: 10.2144/btn-2020-0015] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Resistance is induced in cotton plants as the result of either viral infection or exogenous application of elicitors. Induced resistance can be evaluated by determining the production of β-1,3-glucanase and chitinase in plants as a biochemical parameter. The assays being used for the determination of chitinase and β-1,3-glucanase activity are laborious and not cost-effective, as the reducing sugars produced by the substrates colloidal chitin and laminarin are very expensive. The concentration of both substrates was standardized and reduced to 0.25% from 4% in a modified microplate assay, which appeared to be more effective. The amount of β-1,3-glucanase and chitinase produced was significant and determined by the new modified assay. The sensitivity of the microplate assay was significantly raised approximately one- to twofold.
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Kataria R, Duhan N, Kaundal R. Computational Systems Biology of Alfalfa - Bacterial Blight Host-Pathogen Interactions: Uncovering the Complex Molecular Networks for Developing Durable Disease Resistant Crop. FRONTIERS IN PLANT SCIENCE 2021; 12:807354. [PMID: 35251063 PMCID: PMC8891223 DOI: 10.3389/fpls.2021.807354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/29/2021] [Indexed: 05/04/2023]
Abstract
Medicago sativa (also known as alfalfa), a forage legume, is widely cultivated due to its high yield and high-value hay crop production. Infectious diseases are a major threat to the crops, owing to huge economic losses to the agriculture industry, worldwide. The protein-protein interactions (PPIs) between the pathogens and their hosts play a critical role in understanding the molecular basis of pathogenesis. Pseudomonas syringae pv. syringae ALF3 suppresses the plant's innate immune response by secreting type III effector proteins into the host cell, causing bacterial stem blight in alfalfa. The alfalfa-P. syringae system has little information available for PPIs. Thus, to understand the infection mechanism, we elucidated the genome-scale host-pathogen interactions (HPIs) between alfalfa and P. syringae using two computational approaches: interolog-based and domain-based method. A total of ∼14 M putative PPIs were predicted between 50,629 alfalfa proteins and 2,932 P. syringae proteins by combining these approaches. Additionally, ∼0.7 M consensus PPIs were also predicted. The functional analysis revealed that P. syringae proteins are highly involved in nucleotide binding activity (GO:0000166), intracellular organelle (GO:0043229), and translation (GO:0006412) while alfalfa proteins are involved in cellular response to chemical stimulus (GO:0070887), oxidoreductase activity (GO:0016614), and Golgi apparatus (GO:0005794). According to subcellular localization predictions, most of the pathogen proteins targeted host proteins within the cytoplasm and nucleus. In addition, we discovered a slew of new virulence effectors in the predicted HPIs. The current research describes an integrated approach for deciphering genome-scale host-pathogen PPIs between alfalfa and P. syringae, allowing the researchers to better understand the pathogen's infection mechanism and develop pathogen-resistant lines.
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Affiliation(s)
- Raghav Kataria
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Naveen Duhan
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
| | - Rakesh Kaundal
- Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States
- Bioinformatics Facility, Center for Integrated Biosystems, Utah State University, Logan, UT, United States
- Department of Computer Science, College of Science, Utah State University, Logan, UT, United States
- *Correspondence: Rakesh Kaundal, ;
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Bianchini G, Sánchez‐Baracaldo P. sMap: Evolution of independent, dependent and conditioned discrete characters in a Bayesian framework. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13540] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Zhou Q, Galindo-González L, Manolii V, Hwang SF, Strelkov SE. Comparative Transcriptome Analysis of Rutabaga ( Brassica napus) Cultivars Indicates Activation of Salicylic Acid and Ethylene-Mediated Defenses in Response to Plasmodiophora brassicae. Int J Mol Sci 2020; 21:ijms21218381. [PMID: 33171675 PMCID: PMC7664628 DOI: 10.3390/ijms21218381] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 01/04/2023] Open
Abstract
Clubroot, caused by Plasmodiophora brassicae Woronin, is an important soilborne disease of Brassica napus L. and other crucifers. To improve understanding of the mechanisms of resistance and pathogenesis in the clubroot pathosystem, the rutabaga (B. napus subsp. rapifera Metzg) cultivars ‘Wilhelmsburger’ (resistant) and ‘Laurentian’ (susceptible) were inoculated with P. brassicae pathotype 3A and their transcriptomes were analyzed at 7, 14, and 21 days after inoculation (dai) by RNA sequencing (RNA-seq). Thousands of transcripts with significant changes in expression were identified in each host at each time-point in inoculated vs. non-inoculated plants. Molecular responses at 7 and 14 dai supported clear differences in the clubroot response mechanisms of the two genotypes. Both the resistant and the susceptible cultivars activated receptor-like protein (RLP) genes, resistance (R) genes, and genes involved in salicylic acid (SA) signaling as clubroot defense mechanisms. In addition, genes related to calcium signaling and genes encoding leucine-rich repeat (LRR) receptor kinases, the respiratory burst oxidase homolog (RBOH) protein, and transcription factors such as WRKYs, ethylene responsive factors, and basic leucine zippers (bZIPs), appeared to be upregulated in ‘Wilhelmsburger’ to restrict P. brassicae development. Some of these genes are essential components of molecular defenses, including ethylene (ET) signaling and the oxidative burst. Our study highlights the importance of activation of genes associated with SA- and ET-mediated responses in the resistant cultivar. A set of candidate genes showing contrasting patterns of expression between the resistant and susceptible cultivars was identified and includes potential targets for further study and validation through approaches such as gene editing.
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14
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Zheng T, Zhang K, Sadeghnezhad E, Jiu S, Zhu X, Dong T, Liu Z, Guan L, Jia H, Fang J. Chitinase family genes in grape differentially expressed in a manner specific to fruit species in response to Botrytis cinerea. Mol Biol Rep 2020; 47:7349-7363. [PMID: 32914265 DOI: 10.1007/s11033-020-05791-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/28/2020] [Indexed: 01/03/2023]
Abstract
Chitinases (Chi), an important resistance-related protein, act against fungal pathogens by catalyzing the fungal cell wall, whereas are involved in different biological pathways in grape. In this study, we found 42 Chi family genes in Vitis vinifera L. (VvChis) and evaluated their expression levels after Botrytis infection, stress hormones like ethylene (ETH) and methyl-jasmonate (MeJA), and abiotic stresses like salinity and temperature changes in ripened fruits. VvChis were categorized into five groups including A, B, C, D, and E belonged to glycoside hydrolase family 18 and 19 (GH18 and GH19) according to genes structure, which expression analysis showed distinct temporal and spatial expression patterns changed in different tissues and various development stages. Different responsive elements to biotic and abiotic stresses were determined in the promoter regions of VvChis, specially elicitor-responsive element that was conserved among all VvChis genes. The expression levels of VvChis in groups A, B, and E increased after Botrytis cinerea infection in leaves and berries. Meanwhile, VvChis in glycoside hydrolase family 18 (GH18) were up-regulated under MeJA and ETH treatment, although the induction of VvChis by low temperature was more significant than high temperature. The expression of VvChis was also positively correlated with the concentration of NaCl treatment. Furthermore, differential gene-overexpression of VvChi5, VvChi17, VvChi22, VvChi26, and VvChi31 in strawberry and tomato fruits demonstrated the involvement of various isoforms in resistance to Botrytis infection through antioxidant system and lignin accumulation, which led to a reduction of damage. Among different isoforms of VvChis, we confirmed the interaction of Chi17 with Metallothionein (MTL) as oxidative stress protection, which suggests VvChis can modulate oxidative stress during postharvest storage in ripened fruits.
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Affiliation(s)
- Ting Zheng
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Kekun Zhang
- College of Enology, Northwest A&F University, Yangling, 712100, People's Republic of China
| | - Ehsan Sadeghnezhad
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Songtao Jiu
- Department of Plant Science, Shanghai Jiao Tong University, Shanghai City, 200030, Shanghai, People's Republic of China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Tianyu Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Zhongjie Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Le Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China
| | - Haifeng Jia
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China.
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing City, 210095, Jiangsu Province, People's Republic of China.
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15
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Man J, Gallagher JP, Bartlett M. Structural evolution drives diversification of the large LRR-RLK gene family. THE NEW PHYTOLOGIST 2020; 226:1492-1505. [PMID: 31990988 PMCID: PMC7318236 DOI: 10.1111/nph.16455] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/19/2020] [Indexed: 05/11/2023]
Abstract
●Cells are continuously exposed to chemical signals that they must discriminate between and respond to appropriately. In embryophytes, the leucine-rich repeat receptor-like kinases (LRR-RLKs) are signal receptors critical in development and defense. LRR-RLKs have diversified to hundreds of genes in many plant genomes. Although intensively studied, a well-resolved LRR-RLK gene tree has remained elusive. ●To resolve the LRR-RLK gene tree, we developed an improved gene discovery method based on iterative hidden Markov model searching and phylogenetic inference. We used this method to infer complete gene trees for each of the LRR-RLK subclades and reconstructed the deepest nodes of the full gene family. ●We discovered that the LRR-RLK gene family is even larger than previously thought, and that protein domain gains and losses are prevalent. These structural modifications, some of which likely predate embryophyte diversification, led to misclassification of some LRR-RLK variants as members of other gene families. Our work corrects this misclassification. ●Our results reveal ongoing structural evolution generating novel LRR-RLK genes. These new genes are raw material for the diversification of signaling in development and defense. Our methods also enable phylogenetic reconstruction in any large gene family.
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Affiliation(s)
- Jarrett Man
- Biology DepartmentUniversity of Massachusetts Amherst611 North Pleasant Street, 221 Morrill 3AmherstMA01003USA
| | - Joseph P. Gallagher
- Biology DepartmentUniversity of Massachusetts Amherst611 North Pleasant Street, 221 Morrill 3AmherstMA01003USA
| | - Madelaine Bartlett
- Biology DepartmentUniversity of Massachusetts Amherst611 North Pleasant Street, 221 Morrill 3AmherstMA01003USA
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16
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Sierra-Gómez Y, Rodríguez-Hernández A, Cano-Sánchez P, Gómez-Velasco H, Hernández-Santoyo A, Siliqi D, Rodríguez-Romero A. A biophysical and structural study of two chitinases from Agave tequilana and their potential role as defense proteins. FEBS J 2019; 286:4778-4796. [PMID: 31291689 DOI: 10.1111/febs.14993] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 05/04/2019] [Accepted: 07/08/2019] [Indexed: 01/09/2023]
Abstract
Plant chitinases are enzymes that have several functions, including providing protection against pathogens. Agave tequilana is an economically important plant that is poorly studied. Here, we identified a chitinase from short reads of the A. tequilana transcriptome (AtChi1). A second chitinase, differing by only six residues from the first, was isolated from total RNA of plants infected with Fusarium oxysporum (AtChi2). Both enzymes were overexpressed in Escherichia coli and analysis of their sequences indicated that they belong to the class I glycoside hydrolase family19, whose members exhibit two domains: a carbohydrate-binding module and a catalytic domain, connected by a flexible linker. Activity assays and thermal shift experiments demonstrated that the recombinant Agave enzymes are highly thermostable acidic endochitinases with Tm values of 75 °C and 71 °C. Both exhibit a molecular mass close to 32 kDa, as determined by MALDI-TOF, and experimental pIs of 3.7 and 3.9. Coupling small-angle x-ray scattering information with homology modeling and docking simulations allowed us to structurally characterize both chitinases, which notably show different interactions in the binding groove. Even when the six different amino acids are all exposed to solvent in the loops located near the linker and opposite to the binding site, they confer distinct kinetic parameters against colloidal chitin and similar affinity for (GlnNAc)6, as shown by isothermal titration calorimetry. Interestingly, binding is more enthalpy-driven for AtChi2. Whereas the physiological role of these chitinases remains unknown, we demonstrate that they exhibit important antifungal activity against chitin-rich fungi such as Aspergillus sp. DATABASE: SAXS structural data are available in the SASBDB database with accession numbers SASDDE7 and SASDDA6. ENZYMES: Chitinases (EC3.2.1.14).
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Affiliation(s)
- Yusvel Sierra-Gómez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Patricia Cano-Sánchez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Homero Gómez-Velasco
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Dritan Siliqi
- Istituto di Cristallografia, Consiglio Nazionale delle Ricerche, Bari, Italy
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17
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Xu J, Li Y, Lv Y, Bian C, You X, Endoh D, Teraoka H, Shi Q. Molecular Evolution of Tryptophan Hydroxylases in Vertebrates: A Comparative Genomic Survey. Genes (Basel) 2019; 10:genes10030203. [PMID: 30857219 PMCID: PMC6470480 DOI: 10.3390/genes10030203] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 02/19/2019] [Accepted: 03/04/2019] [Indexed: 02/02/2023] Open
Abstract
Serotonin is a neurotransmitter involved in various physiological processes in the central and peripheral nervous systems. Serotonin is also a precursor for melatonin biosynthesis, which mainly occurs in the pineal gland of vertebrates. Tryptophan hydroxylase (TPH) acts as the rate-limiting enzyme in serotonin biosynthesis and is the initial enzyme involved in the synthesis of melatonin. Recently, two enzymes—TPH1 and TPH2—were reported to form the TPH family in vertebrates and to play divergent roles in serotonergic systems. Here, we examined the evolution of the TPH family from 70 vertebrate genomes. Based on the sequence similarity, we extracted 184 predicted tph homologs in the examined vertebrates. A phylogenetic tree, constructed on the basis of these protein sequences, indicated that tph genes could be divided into two main clades (tph1 and tph2), and that the two clades were further split into two subgroups of tetrapods and Actinopterygii. In tetrapods, and some basal non-teleost ray-finned fishes, only two tph isotypes exist. Notably, tph1 in most teleosts that had undergone the teleost-specific genome duplication could be further divided into tph1a and tph1b. Moreover, protein sequence comparisons indicated that TPH protein changes among vertebrates were concentrated at the NH2-terminal. The tertiary structures of TPH1 and TPH2 revealed obvious differences in the structural elements. Five positively selected sites were characterized in TPH2 compared with TPH1; these sites may reflect the functional divergence in enzyme activity and substrate specificity. In summary, our current work provides novel insights into the evolution of tph genes in vertebrates from a comprehensive genomic perspective.
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Affiliation(s)
- Junmin Xu
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Yanping Li
- BGI-Shenzhen, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Yunyun Lv
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
| | - Daiji Endoh
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Hiroki Teraoka
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu 069-8501, Japan.
| | - Qiong Shi
- BGI-Shenzhen, Shenzhen 518083, China.
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, BGI, Shenzhen 518083, China.
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen 518083, China.
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18
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Cao J, Tan X. Comprehensive Analysis of the Chitinase Family Genes in Tomato ( Solanum lycopersicum). PLANTS 2019; 8:plants8030052. [PMID: 30823433 PMCID: PMC6473868 DOI: 10.3390/plants8030052] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Revised: 02/22/2019] [Accepted: 02/22/2019] [Indexed: 12/19/2022]
Abstract
Chitinase catalyzes the hydrolysis of chitin β-1,4 linkages. However, plants cannot produce chitin, suggesting that plant chitinases do not have the same function as animals. This study investigated the chitinase gene family in tomato and divided into eight groups via phylogenetic analyses with Arabidopsis and rice members. Conserved gene structures and motif arrangements indicated their functional relevance with each group. These genes were nonrandomly distributed across the tomato chromosomes, and tandem duplication contributed to the expansion of this gene family. Synteny analysis also established orthology relationships and functional linkages between Arabidopsis and tomato chitinase genes. Several positive selection sites were identified, which may contribute to the functional divergence of the protein family in evolution. In addition, differential expression profiles of the tomato chitinase genes were also investigated at some developmental stages, or under different biotic and abiotic stresses. Finally, functional network analysis found 124 physical or functional interactions, implying the diversity of physiological functions of the family proteins. These results provide a foundation for the exploration of the chitinase genes in plants and will offer some insights for further functional studies.
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Affiliation(s)
- Jun Cao
- Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, China.
| | - Xiaona Tan
- Institute of Life Sciences, Jiangsu University, Xuefu Road 301, Zhenjiang 212013, China.
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19
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Abstract
While epidemiological models have traditionally assumed that diseases spread by the mass action principle, actual contact networks within social groups do not meet this assumption. Theoretical models have shown that disease dynamics could vary considerably under different types of contact networks, but these models face challenges in terms of their evaluation due to the difficulty of collecting empirical data. The honeybee colony with its elaborate social organization and large repertoire of diseases provides an ideal setting to explore how the structure of the contact network contributes to the transmission of a disease.
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20
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Prunier J, Giguère I, Ryan N, Guy R, Soolanayakanahally R, Isabel N, MacKay J, Porth I. Gene copy number variations involved in balsam poplar (Populus balsamifera L.) adaptive variations. Mol Ecol 2018; 28:1476-1490. [PMID: 30270494 DOI: 10.1111/mec.14836] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 12/12/2022]
Abstract
Gene copy number variations (CNVs) involved in phenotypic variations have already been shown in plants, but genomewide testing of CNVs for adaptive variation was not doable until recent technological developments. Thus, reports of the genomic architecture of adaptation involving CNVs remain scarce to date. Here, we investigated F1 progenies of an intraprovenance cross (north-north cross, 58th parallel) and an interprovenances cross (north-south cross, 58th/49th parallels) for CNVs using comparative genomic hybridization on arrays of probes targeting gene sequences in balsam poplar (Populus balsamifera L.), a widespread North American forest tree. A total of 1,721 genes were found in varying copy numbers over the set of 19,823 tested genes. These gene CNVs presented an estimated average size of 8.3 kb and were distributed over poplar's 19 chromosomes including 22 hotspot regions. Gene CNVs number was higher for the interprovenance progeny in accordance with an expected higher genetic diversity related to the composite origin of this family. Regression analyses between gene CNVs and seven adaptive trait variations resulted in 23 significant links; among these adaptive gene CNVs, 30% were located in hotspots. One-to-five gene CNVs were found related to each of the measured adaptive traits and annotated for both biotic and abiotic stress responses. These annotations can be related to the occurrence of a higher pathogenic pressure in the southern parts of balsam poplar's distribution, and higher photosynthetic assimilation rates and water-use efficiency at high latitudes. Overall, our findings suggest that gene CNVs typically having higher mutation rates than SNPs may in fact represent efficient adaptive variations against fast-evolving pathogens.
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Affiliation(s)
- Julien Prunier
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
| | - Isabelle Giguère
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
| | - Natalie Ryan
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Guy
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Raju Soolanayakanahally
- Indian Head Research Farm, Agriculture and Agri-Food Canada, Indian Head, Saskatchewan, Canada
| | - Nathalie Isabel
- Laurentian Forest Centre, Canadian Forest Service, Natural Resources Canada, Québec, Quebec, Canada
| | - John MacKay
- Department of Plant Sciences, University of Oxford, Oxford, UK
| | - Ilga Porth
- Institute for System and Integrated Biology (IBIS), Université Laval, Québec, Québec, Canada.,Centre for Forest Research, Université Laval, Québec, Quebec, Canada
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21
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Changes in salicylic acid content and pathogenesis - related (PR2) gene expression during barley - Pyrenophora teres interaction. ACTA ACUST UNITED AC 2018. [DOI: 10.2478/hppj-2018-0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Abstract
Net blotch (NB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres, substantially reduces barley grain yield and quality worldwide. The role of salicylic acid (SA) signaling in NB resistance has been poorly documented. In this study, SA levels as well as the expression of the SA-responsive gene PR2 were monitored in infected leaves of two barley genotypes, Banteng (resistant) and WI2291 (susceptible), at different time points of infection. SA signaling was activated in bothgenotypes 24 hours post infection (hpi) as compared with non-inoculated plants. However, with or without pathogen pretreatment, SA signifi cantly increased (P=0.001) in Banteng comparing with WI2291. RT-PCR analysis revealed that PR2 expression increases in the resistant and susceptible genotypes over the inoculation time points, with maximum expression (6.4 and 1.99-fold, respectively) observed 6 dpi. PR2 expression was paralleled by an increase in leaf SA content as shown by the test coincidence (F3, 32 = 4.74, P = 0.001). Based on barley genotype resistance levels, our data strengthen the idea that SA signaling and PR2 play a role in barley NB reduction
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22
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Chan YS, Wong JH, Ng TB. Bioactive Proteins in Panax notoginseng Roots and Other Panax Species. Curr Protein Pept Sci 2018; 20:231-239. [PMID: 29895241 DOI: 10.2174/1389203719666180612083650] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2018] [Revised: 04/10/2018] [Accepted: 05/20/2018] [Indexed: 01/04/2023]
Abstract
The genus Panax consists of a group of prized medicinal herbs. Major members of the Panax genus include P. ginseng, P. notoginseng, P. quinquefolius, and P. vietnamensis. They possess various bioactive constituents such as ginsenosides, saponins, polysaccharides and proteins. Many of them were reported to show beneficial effects on human health. Ginsenosides and saponins of ginsengs caught the sight of most researchers. Precise investigations revealed their roles on improvement of the functioning of the nervous system, cardiovascular system, and other functions. In contrast, our knowledge of the bioactive Panax proteins is relatively limited. A number of proteins from P. ginseng, the most valuable member of Panax species, have been investigated and proved to be beneficial to our body. Meanwhile, a few bioactive P. notoginseng proteins, such as ribonucleases and antifungal proteins, have been characterized and reported. We summarize herein the proteins present in P. notoginseng that have been identified, and try to compare them with those from other Panax species with a similar structure or bioactivity, and conclude whether the proteins in P. notoginseng have any distinctive features.
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Affiliation(s)
- Yau Sang Chan
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Jack Ho Wong
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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23
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Feis ME, John U, Lokmer A, Luttikhuizen PC, Wegner KM. Dual transcriptomics reveals co-evolutionary mechanisms of intestinal parasite infections in blue mussels Mytilus edulis. Mol Ecol 2018; 27:1505-1519. [DOI: 10.1111/mec.14541] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 01/30/2018] [Accepted: 02/06/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Marieke E. Feis
- Department Coastal Ecology; Wadden Sea Station Sylt; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; List/Sylt Germany
| | - Uwe John
- Department Ecological Chemistry; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; Bremerhaven Germany
- Helmholtz Institute for Functional Marine Biodiversity (HIFMB); Oldenburg Germany
| | - Ana Lokmer
- Department Coastal Ecology; Wadden Sea Station Sylt; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; List/Sylt Germany
| | - Pieternella C. Luttikhuizen
- NIOZ Royal Netherlands Institute for Sea Research; Department of Coastal Systems, and Utrecht University; Den Burg The Netherlands
| | - K. Mathias Wegner
- Department Coastal Ecology; Wadden Sea Station Sylt; Alfred Wegener Institute; Helmholtz Centre for Polar and Marine Research; List/Sylt Germany
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24
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Identification of Possibility of Glycyrrhiza uralensis as an Allergen by Protein Analysis. BIOCHIP JOURNAL 2018. [DOI: 10.1007/s13206-017-2110-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Wuyun TN, Wang L, Liu H, Wang X, Zhang L, Bennetzen JL, Li T, Yang L, Liu P, Du L, Wang L, Huang M, Qing J, Zhu L, Bao W, Li H, Du Q, Zhu J, Yang H, Yang S, Liu H, Yue H, Hu J, Yu G, Tian Y, Liang F, Hu J, Wang D, Gao R, Li D, Du H. The Hardy Rubber Tree Genome Provides Insights into the Evolution of Polyisoprene Biosynthesis. MOLECULAR PLANT 2018; 11:429-442. [PMID: 29229569 DOI: 10.1016/j.molp.2017.11.014] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 11/14/2017] [Accepted: 11/28/2017] [Indexed: 05/21/2023]
Abstract
Eucommia ulmoides, also called hardy rubber tree, is an economically important tree; however, the lack of its genome sequence restricts the fundamental biological research and applied studies of this plant species. Here, we present a high-quality assembly of its ∼1.2-Gb genome (scaffold N50 = 1.88 Mb) with at least 26 723 predicted genes for E. ulmoides, the first sequenced genome of the order Garryales, which was obtained using an integrated strategy combining Illumina sequencing, PacBio sequencing, and BioNano mapping. As a sister taxon to lamiids and campanulids, E. ulmoides underwent an ancient genome triplication shared by core eudicots but no further whole-genome duplication in the last ∼125 million years. E. ulmoides exhibits high expression levels and/or gene number expansion for multiple genes involved in stress responses and the biosynthesis of secondary metabolites, which may account for its considerable environmental adaptability. In contrast to the rubber tree (Hevea brasiliensis), which produces cis-polyisoprene, E. ulmoides has evolved to synthesize long-chain trans-polyisoprene via farnesyl diphosphate synthases (FPSs). Moreover, FPS and rubber elongation factor/small rubber particle protein gene families were expanded independently from the H. brasiliensis lineage. These results provide new insights into the biology of E. ulmoides and the origin of polyisoprene biosynthesis.
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Affiliation(s)
- Ta-Na Wuyun
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China.
| | - Lin Wang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Huimin Liu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | | | - Tiezhu Li
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lirong Yang
- Institute of Plant Protection Research, Henan Academy of Agricultural Sciences, Zhengzhou 450003, China
| | - Panfeng Liu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lanying Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lu Wang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Mengzhen Huang
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Jun Qing
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Lili Zhu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Wenquan Bao
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Hongguo Li
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Qingxin Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Jingle Zhu
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China
| | - Hong Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Shuguang Yang
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Hui Liu
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China
| | - Hui Yue
- Shandong BELO EUCOMMIA Biological Engineering Co., Ltd., Qingzhou 262500, China
| | - Jiang Hu
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Guoliang Yu
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Yu Tian
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Fan Liang
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Jingjing Hu
- Wuhan Unique Gene Bioinformatics Science and Technology Co., Ltd., Wuhan 430073, China
| | - Depeng Wang
- Nextomics Biosciences Co., Ltd., Wuhan 430073, China
| | - Ruiwen Gao
- Shandong BELO EUCOMMIA Biological Engineering Co., Ltd., Qingzhou 262500, China.
| | - Dejun Li
- Key Laboratory of Biology and Genetic Resources of Rubber Tree, Ministry of Agriculture, Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou 571737, China.
| | - Hongyan Du
- Non-timber Forest Research and Development Center, Chinese Academy of Forestry, Zhengzhou 450003, China; The Eucommia Engineering Research Center of State Forestry Administration, Zhengzhou 450003, China.
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Chitinase-like proteins as regulators of innate immunity and tissue repair: helpful lessons for asthma? Biochem Soc Trans 2018; 46:141-151. [PMID: 29351964 DOI: 10.1042/bst20170108] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 11/17/2017] [Accepted: 11/23/2017] [Indexed: 12/19/2022]
Abstract
Chitinases and chitinase-like proteins (CLPs) belong to the glycoside hydrolase family 18 of proteins. Chitinases are expressed in mammals and lower organisms, facilitate chitin degradation, and hence act as host-defence enzymes. Gene duplication and loss-of-function mutations of enzymatically active chitinases have resulted in the expression of a diverse range of CLPs across different species. CLPs are genes that are increasingly associated with inflammation and tissue remodelling not only in mammals but also across distant species. While the focus has remained on understanding the functions and expression patterns of CLPs during disease in humans, studies in mouse and lower organisms have revealed important and overlapping roles of the CLP family during physiology, host defence and pathology. This review will summarise recent insights into the regulatory functions of CLPs on innate immune pathways and discuss how these effects are not only important for host defence and tissue injury/repair after pathogen invasion, but also how they have extensive implications for pathological processes involved in diseases such as asthma.
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Mondragón-Palomino M, Stam R, John-Arputharaj A, Dresselhaus T. Diversification of defensins and NLRs in Arabidopsis species by different evolutionary mechanisms. BMC Evol Biol 2017; 17:255. [PMID: 29246101 PMCID: PMC5731061 DOI: 10.1186/s12862-017-1099-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 11/24/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Genes encoding proteins underlying host-pathogen co-evolution and which are selected for new resistance specificities frequently are under positive selection, a process that maintains diversity. Here, we tested the contribution of natural selection, recombination and transcriptional divergence to the evolutionary diversification of the plant defensins superfamily in three Arabidopsis species. The intracellular NOD-like receptor (NLR) family was used for comparison because positive selection has been well documented in its members. Similar to defensins, NLRs are encoded by a large and polymorphic gene family and many of their members are involved in the immune response. RESULTS Gene trees of Arabidopsis defensins (DEFLs) show a high prevalence of clades containing orthologs. This indicates that their diversity dates back to a common ancestor and species-specific duplications did not significantly contribute to gene family expansion. DEFLs are characterized by a pervasive pattern of neutral evolution with infrequent positive and negative selection as well as recombination. In comparison, most NLR alignment groups are characterized by frequent occurrence of positive selection and recombination in their leucine-rich repeat (LRR) domain as well negative selection in their nucleotide-binding (NB-ARC) domain. While major NLR subgroups are expressed in pistils and leaves both in presence or absence of pathogen infection, the members of DEFL alignment groups are predominantly transcribed in pistils. Furthermore, conserved groups of NLRs and DEFLs are differentially expressed in response to Fusarium graminearum regardless of whether these genes are under positive selection or not. CONCLUSIONS The present analyses of NLRs expands previous studies in Arabidopsis thaliana and highlights contrasting patterns of purifying and diversifying selection affecting different gene regions. DEFL genes show a different evolutionary trend, with fewer recombination events and significantly fewer instances of natural selection. Their heterogeneous expression pattern suggests that transcriptional divergence probably made the major contribution to functional diversification. In comparison to smaller families encoding pathogenesis-related (PR) proteins under positive selection, DEFLs are involved in a wide variety of processes that altogether might pose structural and functional trade-offs to their family-wide pattern of evolution.
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Affiliation(s)
- Mariana Mondragón-Palomino
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätstraße 31, 93053, Regensburg, Germany.
| | - Remco Stam
- Chair of Phytopathology, Technical University of Munich, School of Life Sciences Weihenstephan, Emil-Ramann-Str. 2, 85354, Freising, Germany
| | - Ajay John-Arputharaj
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätstraße 31, 93053, Regensburg, Germany
| | - Thomas Dresselhaus
- Cell Biology and Plant Biochemistry, Biochemie-Zentrum Regensburg, University of Regensburg, Universitätstraße 31, 93053, Regensburg, Germany
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Song K, Li Y, Huang B, Li L, Zhang G. Genetic and evolutionary patterns of innate immune genes in the Pacific oyster Crassostrea gigas. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:17-22. [PMID: 28711462 DOI: 10.1016/j.dci.2017.07.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/11/2017] [Accepted: 07/11/2017] [Indexed: 06/07/2023]
Abstract
The invertebrate innate immune system functions in immune defence and the stress response. However, knowledge of the genetic and evolutionary patterns of innate immune genes in Mollusca is limited, especially for oysters. Such information would help clarify how oysters adapt to pathogen-rich environments. Here, we characterized the genetic and evolutionary patterns of the innate immune genes in Crassostrea gigas, using population diversity analysis and evolution rates comparison. Innate immune genes have higher median nucleotide diversity than non-immune genes. Nucleotide diversity varied with functional regions and different immune-related gene families. Evolutionary analysis of two Crassostrea species showed that the innate immune genes are less conserved and have higher rates of evolution in C. gigas. We also noted a positive association between nucleotide diversity and selective pressures for genes having orthologues. Our findings will help determine the evolutionary patterns of innate immune genes and the association of these genes with mollusc immunity.
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Affiliation(s)
- Kai Song
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, 266071, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Yingxiang Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Baoyu Huang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, 266071, China; Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China.
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, 266071, China; National & Local Joint Engineering Laboratory of Ecological Mariculture, Qingdao, Shandong, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266071, China.
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Ma S, Song Q, Tao H, Harrison A, Wang S, Liu W, Lin S, Zhang Z, Ai Y, He H. Prediction of protein–protein interactions between fungus (Magnaporthe grisea) and rice (Oryza sativa L.). Brief Bioinform 2017; 20:448-456. [DOI: 10.1093/bib/bbx132] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/15/2017] [Indexed: 12/13/2022] Open
Affiliation(s)
- Shiwei Ma
- College of Life Sciences, Fujian Agriculture and Forestry University, China
| | - Qi Song
- College of Life Sciences, Fujian Agriculture and Forestry University, China
| | - Huan Tao
- College of Life Sciences, Fujian Agriculture and Forestry University, China
| | - Andrew Harrison
- Department of Mathematical Sciences, University of Essex, UK
| | - Shaobo Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, China
| | - Wei Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, China
| | - Shoukai Lin
- Fujian Provincial Key Laboratory of Ecology-toxicological Effects and Control for Emerging Contaminants, Putian University
| | - Ziding Zhang
- College of Biological Sciences, China Agriculture University, China
| | - Yufang Ai
- College of Life Sciences, Fujian Agriculture and Forestry University, China
| | - Huaqin He
- College of Life Sciences, Fujian Agriculture and Forestry University, China
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31
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Ma XL, Milne RI, Zhou HX, Fang JY, Zha HG. Floral nectar of the obligate outcrossing Canavalia gladiata (Jacq.) DC. (Fabaceae) contains only one predominant protein, a class III acidic chitinase. PLANT BIOLOGY (STUTTGART, GERMANY) 2017; 19:749-759. [PMID: 28544154 DOI: 10.1111/plb.12583] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/15/2017] [Indexed: 06/07/2023]
Abstract
Floral nectar can affect the fitness of insect-pollinated plants, through both attraction and manipulation of pollinators. Self-incompatible insect-pollinated plants receive more insect visits than their self-compatible relatives, and the nectar of such species might face increased risk of infestation by pathogens carried by pollinators than self-compatible plants. Proteins in nectar (nectarins) play an important role in protecting the nectar, but little is known regarding nectarins in self-incompatible species. The nectarins from a self-incompatible and insect-pollinated leguminous crop, Canavalia gladiata, were separated using two-dimensional electrophoresis and analysed using mass spectrometry. The predominant nectarin gene was cloned and the gene expression pattern investigated using quantitative real-time PCR. Chitinolytic activity in the nectar was tested with different substrates. The C. gladiata nectar proteome only has one predominant nectarin, an acidic class III chitinase (CaChi3). The full-length CaChi3 gene was cloned, coding for a protein of 298 amino acids with a predicted signal peptide. CaChi3 is very similar to members of the class III chitinase family, whose evolution is dominated by purifying selection. CaChi3 was expressed in both nectary and leaves. CaChi3 has thermostable chitinolytic activity according to glycol-chitin zymography or a fluorogenic substratem but has no lysozyme activity. Chitinase might be a critical protein component in nectar. The extremely simple nectar proteome in C. gladiata disproves the hypothesis that self-incompatible species always have more complex nectar proteomes. Accessibility of nectar might be a significant determinant of the evolutionary pressure to develop nectar defence mechanisms.
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Affiliation(s)
- X L Ma
- College of Life and Environment Sciences, Huangshan University, Anhui, China
| | - R I Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
- Royal Botanic Garden, Edinburgh, UK
| | - H X Zhou
- College of Life and Environment Sciences, Huangshan University, Anhui, China
| | - J Y Fang
- College of Life and Environment Sciences, Huangshan University, Anhui, China
| | - H G Zha
- College of Life and Environment Sciences, Huangshan University, Anhui, China
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Huang Z, Young ND, Reagon M, Hyma KE, Olsen KM, Jia Y, Caicedo AL. All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian
Oryza. Mol Ecol 2017; 26:3151-3167. [DOI: 10.1111/mec.14120] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 01/21/2017] [Accepted: 03/10/2017] [Indexed: 01/28/2023]
Affiliation(s)
- Zhongyun Huang
- Department of Biology University of Massachusetts Amherst MA USA
| | - Nelson D. Young
- Department of Biology University of Massachusetts Amherst MA USA
| | - Michael Reagon
- Department of Biology Ohio State University Lima Lima OH USA
| | - Katie E. Hyma
- Department of Biology University of Massachusetts Amherst MA USA
| | | | - Yulin Jia
- Dale Bumpers National Rice Research Center USDA‐ARS Stuttgart AR USA
| | - Ana L. Caicedo
- Department of Biology University of Massachusetts Amherst MA USA
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Tobias PA, Christie N, Naidoo S, Guest DI, Külheim C. Identification of the Eucalyptus grandis chitinase gene family and expression characterization under different biotic stress challenges. TREE PHYSIOLOGY 2017; 37:565-582. [PMID: 28338992 DOI: 10.1093/treephys/tpx010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 02/06/2017] [Indexed: 06/06/2023]
Abstract
Eucalyptus grandis (W. Hill ex Maiden) is an Australian Myrtaceae tree grown for timber in many parts of the world and for which the annotated genome sequence is available. Known to be susceptible to a number of pests and diseases, E. grandis is a useful study organism for investigating defense responses in woody plants. Chitinases are widespread in plants and cleave glycosidic bonds of chitin, the major structural component of fungal cell walls and arthropod exoskeletons. They are encoded by an important class of genes known to be up-regulated in plants in response to pathogens. The current study identified 67 chitinase gene models from two families known as glycosyl hydrolase 18 and 19 (36 GH18 and 31 GH19) within the E. grandis genome assembly (v1.1), indicating a recent gene expansion. Sequences were aligned and analyzed as conforming to currently recognized plant chitinase classes (I-V). Unlike other woody species investigated to date, E. grandis has a single gene encoding a putative vacuolar targeted Class I chitinase. In response to Leptocybe invasa (Fisher & La Salle) (the eucalypt gall wasp) and Chrysoporthe austroafricana (Gryzenhout & M.J. Wingf. 2004) (causal agent of fungal stem canker), this Class IA chitinase is strongly up-regulated in both resistant and susceptible plants. Resistant plants, however, indicate greater constitutive expression and increased up-regulation than susceptible plants following fungal challenge. Up-regulation within fungal resistant clones was further confirmed with protein data. Clusters of putative chitinase genes, particularly on chromosomes 3 and 8, are significantly up-regulated in response to fungal challenge, while a cluster on chromosome 1 is significantly down-regulated in response to gall wasp. The results of this study show that the E. grandis genome has an expanded group of chitinase genes, compared with other plants. Despite this expansion, only a single Class I chitinase is present and this gene is highly up-regulated within diverse biotic stress conditions. Our research provides insight into a major class of defense genes within E. grandis and indicates the importance of the Class I chitinase.
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Affiliation(s)
- Peri A Tobias
- School of Life and Environmental Science, Sydney Institute of Agriculture, University of Sydney, Eveleigh, NSW 2015, Australia
| | - Nanette Christie
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
| | - David I Guest
- School of Life and Environmental Science, Sydney Institute of Agriculture, University of Sydney, Eveleigh, NSW 2015, Australia
| | - Carsten Külheim
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
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Rovenich H, Zuccaro A, Thomma BPHJ. Convergent evolution of filamentous microbes towards evasion of glycan-triggered immunity. THE NEW PHYTOLOGIST 2016; 212:896-901. [PMID: 27329426 DOI: 10.1111/nph.14064] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/12/2016] [Indexed: 05/20/2023]
Abstract
896 I. 896 II. 896 III. 897 IV. 898 V. 899 VI. 899 900 References 900 SUMMARY: All filamentous microbes produce and release a wide range of glycans, which are essential determinants of microbe-microbe and microbe-host interactions. Major cell wall constituents, such as chitin and β-glucans, are elicitors of host immune responses. The widespread capacity for glycan perception in plants has driven the evolution of various strategies that help filamentous microbes to evade detection. Common strategies include structural and chemical modifications of cell wall components as well as the secretion of effector proteins that suppress chitin- and β-glucan-triggered immune responses. Thus, the necessity to avoid glycan-triggered immunity represents a driving force in the convergent evolution of filamentous microbes towards its suppression.
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Affiliation(s)
- Hanna Rovenich
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
| | - Alga Zuccaro
- Botanical Institute, Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, 50674, Cologne, Germany
- Department of Organismic Interactions, Max Planck Institute for Terrestrial Microbiology, 35043, Marburg, Germany
| | - Bart P H J Thomma
- Laboratory of Phytopathology, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands
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35
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Xu J, Xu X, Tian L, Wang G, Zhang X, Wang X, Guo W. Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton. Sci Rep 2016; 6:29022. [PMID: 27354165 PMCID: PMC4926273 DOI: 10.1038/srep29022] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 06/14/2016] [Indexed: 12/02/2022] Open
Abstract
Verticillium dahliae, a destructive and soil-borne fungal pathogen, causes massive losses in cotton yields. However, the resistance mechanism to V. dahilae in cotton is still poorly understood. Accumulating evidence indicates that chitinases are crucial hydrolytic enzymes, which attack fungal pathogens by catalyzing the fungal cell wall degradation. As a large gene family, to date, the chitinase genes (Chis) have not been systematically analyzed and effectively utilized in cotton. Here, we identified 47, 49, 92, and 116 Chis from four sequenced cotton species, diploid Gossypium raimondii (D5), G. arboreum (A2), tetraploid G. hirsutum acc. TM-1 (AD1), and G. barbadense acc. 3-79 (AD2), respectively. The orthologous genes were not one-to-one correspondence in the diploid and tetraploid cotton species, implying changes in the number of Chis in different cotton species during the evolution of Gossypium. Phylogenetic classification indicated that these Chis could be classified into six groups, with distinguishable structural characteristics. The expression patterns of Chis indicated their various expressions in different organs and tissues, and in the V. dahliae response. Silencing of Chi23, Chi32, or Chi47 in cotton significantly impaired the resistance to V. dahliae, suggesting these genes might act as positive regulators in disease resistance to V. dahliae.
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Affiliation(s)
- Jun Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoyang Xu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Liangliang Tian
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Guilin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xueying Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
| | - Xinyu Wang
- College of Life Science, Nanjing Agricultural University, Nanjing 210095, China
| | - Wangzhen Guo
- State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R&D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China
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Gasch AP, Payseur BA, Pool JE. The Power of Natural Variation for Model Organism Biology. Trends Genet 2016; 32:147-154. [PMID: 26777596 PMCID: PMC4769656 DOI: 10.1016/j.tig.2015.12.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/09/2015] [Accepted: 12/14/2015] [Indexed: 11/24/2022]
Abstract
Genetic background effects have long been recognized and, in some cases studied, but they are often viewed as a nuisance by molecular biologists. We suggest that genetic variation currently represents a critical frontier for molecular studies. Human genetics has seen a surge of interest in genetic variation and its contributions to disease, but insights into disease mechanisms are difficult since information about gene function is lacking. By contrast, model organism genetics has excelled at revealing molecular mechanisms of cellular processes, but often de-emphasizes genetic variation and its functional consequences. We argue that model organism biology would benefit from incorporating natural variation, both to capture how well laboratory lines exemplify the species they represent and to inform on molecular processes and their variability. Such a synthesis would also greatly expand the relevance of model systems for studies of complex trait variation, including disease.
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Affiliation(s)
- Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Bret A Payseur
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - John E Pool
- Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Rausher MD, Huang J. Prolonged Adaptive Evolution of a Defensive Gene in the Solanaceae. Mol Biol Evol 2015; 33:143-51. [PMID: 26412446 DOI: 10.1093/molbev/msv205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Although plants and their natural enemies may coevolve for prolonged periods, little is known about how long individual plant defensive genes are involved in the coevolutionary process. We address this issue by examining patterns of selection on the defensive gene threonine deaminase (TD). Tomato (Solanum lycopersicum) has two copies of this gene. One performs the canonical housekeeping function in amino acid metabolism of catalyzing the first reaction in the conversion of threonine to isoleucine. The second copy functions as an antinutritive defense against lepidopteran herbivores by depleting threonine in the insect gut. Wild tobacco (Nicotiana attenuata) also contains a defensive copy. We show that a single copy of TD underwent two or three duplications near the base of the Solanaceae. One copy retains the housekeeping function, whereas a second copy evolved defensive functions. Positive selection occurred on the branch of the TD2 gene tree subtending the common ancestor of the Nicotianoideae and Solanoideae. It also occurred within the Solanoideae clade but not within the Nicotianoideae clade. Finally, it occurred on most branches leading from the common ancestor to S. lycopersicum. Based on recent calibrations of the Solanaceae phylogeny, TD2 experienced adaptive substitutions for a period of 30-50 My. We suggest that the most likely explanation for this result is fluctuating herbivore abundances: When herbivores are rare, relaxed selection increases the likelihood that slightly disadvantageous mutations will be fixed by drift; when herbivores are common, increased selection causes the evolution of compensatory adaptive mutations. Alternative explanations are also discussed.
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Affiliation(s)
| | - Jie Huang
- Department of Biology, Duke University
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Anisimova M. Darwin and Fisher meet at biotech: on the potential of computational molecular evolution in industry. BMC Evol Biol 2015; 15:76. [PMID: 25928234 PMCID: PMC4422139 DOI: 10.1186/s12862-015-0352-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 04/15/2015] [Indexed: 12/22/2022] Open
Abstract
Background Today computational molecular evolution is a vibrant research field that benefits from the availability of large and complex new generation sequencing data – ranging from full genomes and proteomes to microbiomes, metabolomes and epigenomes. The grounds for this progress were established long before the discovery of the DNA structure. Specifically, Darwin’s theory of evolution by means of natural selection not only remains relevant today, but also provides a solid basis for computational research with a variety of applications. But a long-term progress in biology was ensured by the mathematical sciences, as exemplified by Sir R. Fisher in early 20th century. Now this is true more than ever: The data size and its complexity require biologists to work in close collaboration with experts in computational sciences, modeling and statistics. Results Natural selection drives function conservation and adaptation to emerging pathogens or new environments; selection plays key role in immune and resistance systems. Here I focus on computational methods for evaluating selection in molecular sequences, and argue that they have a high potential for applications. Pharma and biotech industries can successfully use this potential, and should take the initiative to enhance their research and development with state of the art bioinformatics approaches. Conclusions This review provides a quick guide to the current computational approaches that apply the evolutionary principles of natural selection to real life problems – from drug target validation, vaccine design and protein engineering to applications in agriculture, ecology and conservation.
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Affiliation(s)
- Maria Anisimova
- Institute of Applied Simulations, School of Life Sciences and Facility Management, Zürich University of Applied Sciences, Einsiedlerstrasse 31a, Wädenswil, 8820, Switzerland. .,Department of Computer Science, ETH, Zurich, Switzerland. .,Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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Van Sluyter SC, McRae JM, Falconer RJ, Smith PA, Bacic A, Waters EJ, Marangon M. Wine protein haze: mechanisms of formation and advances in prevention. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4020-4030. [PMID: 25847216 DOI: 10.1021/acs.jafc.5b00047] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Protein haze is an aesthetic problem in white wines that can be prevented by removing the grape proteins that have survived the winemaking process. The haze-forming proteins are grape pathogenesis-related proteins that are highly stable during winemaking, but some of them precipitate over time and with elevated temperatures. Protein removal is currently achieved by bentonite addition, an inefficient process that can lead to higher costs and quality losses in winemaking. The development of more efficient processes for protein removal and haze prevention requires understanding the mechanisms such as the main drivers of protein instability and the impacts of various wine matrix components on haze formation. This review covers recent developments in wine protein instability and removal and proposes a revised mechanism of protein haze formation.
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Affiliation(s)
- Steven C Van Sluyter
- †The Australian Wine Research Institute, P.O Box 197, Glen Osmond, South Australia 5064, Australia
- §School of BioSciences and the Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
- #Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Jacqui M McRae
- †The Australian Wine Research Institute, P.O Box 197, Glen Osmond, South Australia 5064, Australia
| | - Robert J Falconer
- ΔDepartment of Chemical and Biological Engineering, ChELSI Institute, University of Sheffield, Sheffield S1 3JD, England
| | - Paul A Smith
- †The Australian Wine Research Institute, P.O Box 197, Glen Osmond, South Australia 5064, Australia
| | - Antony Bacic
- §School of BioSciences and the Bio21 Molecular Sciences and Biotechnology Institute, University of Melbourne, Melbourne, Victoria 3010, Australia
| | - Elizabeth J Waters
- †The Australian Wine Research Institute, P.O Box 197, Glen Osmond, South Australia 5064, Australia
- ⊥Australian Grape and Wine Authority, P.O. Box 2733, Adelaide, South Australia 5000, Australia
| | - Matteo Marangon
- †The Australian Wine Research Institute, P.O Box 197, Glen Osmond, South Australia 5064, Australia
- ΠPlumpton College, Ditchling Road, Nr Lewes, East Sussex BN7 3AE, England
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Kesari P, Patil DN, Kumar P, Tomar S, Sharma AK, Kumar P. Structural and functional evolution of chitinase-like proteins from plants. Proteomics 2015; 15:1693-705. [PMID: 25728311 DOI: 10.1002/pmic.201400421] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 01/16/2015] [Accepted: 02/24/2015] [Indexed: 02/06/2023]
Abstract
The plant genome contains a large number of sequences that encode catalytically inactive chitinases referred to as chitinase-like proteins (CLPs). Although CLPs share high sequence and structural homology with chitinases of glycosyl hydrolase 18 (TIM barrel domain) and 19 families, they may lack the binding/catalytic activity. Molecular genetic analysis revealed that gene duplication events followed by mutation in the existing chitinase gene have resulted in the loss of activity. The evidences show that adaptive functional diversification of the CLPs has been achieved through alterations in the flexible regions than in the rigid structural elements. The CLPs plays an important role in the defense response against pathogenic attack, biotic and abiotic stress. They are also involved in the growth and developmental processes of plants. Since the physiological roles of CLPs are similar to chitinase, such mutations have led to plurifunctional enzymes. The biochemical and structural characterization of the CLPs is essential for understanding their roles and to develop potential utility in biotechnological industries. This review sheds light on the structure-function evolution of CLPs from chitinases.
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Affiliation(s)
- Pooja Kesari
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Dipak Narhari Patil
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pramod Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Shailly Tomar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Ashwani Kumar Sharma
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
| | - Pravindra Kumar
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, India
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Wang J, Meng Y, Li B, Ma X, Lai Y, Si E, Yang K, Xu X, Shang X, Wang H, Wang D. Physiological and proteomic analyses of salt stress response in the halophyte Halogeton glomeratus. PLANT, CELL & ENVIRONMENT 2015; 38:655-69. [PMID: 25124288 PMCID: PMC4407928 DOI: 10.1111/pce.12428] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 07/19/2014] [Accepted: 07/23/2014] [Indexed: 05/04/2023]
Abstract
Very little is known about the adaptation mechanism of Chenopodiaceae Halogeton glomeratus, a succulent annual halophyte, under saline conditions. In this study, we investigated the morphological and physiological adaptation mechanisms of seedlings exposed to different concentrations of NaCl treatment for 21 d. Our results revealed that H. glomeratus has a robust ability to tolerate salt; its optimal growth occurs under approximately 100 mm NaCl conditions. Salt crystals were deposited in water-storage tissue under saline conditions. We speculate that osmotic adjustment may be the primary mechanism of salt tolerance in H. glomeratus, which transports toxic ions such as sodium into specific salt-storage cells and compartmentalizes them in large vacuoles to maintain the water content of tissues and the succulence of the leaves. To investigate the molecular response mechanisms to salt stress in H. glomeratus, we conducted a comparative proteomic analysis of seedling leaves that had been exposed to 200 mm NaCl for 24 h, 72 h and 7 d. Forty-nine protein spots, exhibiting significant changes in abundance after stress, were identified using matrix-assisted laser desorption ionization tandem time-of-flight mass spectrometry (MALDI-TOF/TOF MS/MS) and similarity searches across EST database of H. glomeratus. These stress-responsive proteins were categorized into nine functional groups, such as photosynthesis, carbohydrate and energy metabolism, and stress and defence response.
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Affiliation(s)
- Juncheng Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Yaxiong Meng
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Baochun Li
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Life Sciences and Technology, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Xiaole Ma
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Yong Lai
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Erjing Si
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Ke Yang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Xianliang Xu
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Xunwu Shang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
| | - Huajun Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
| | - Di Wang
- Gansu Provincial Key Lab of Aridland Crop Science/Gansu Key Lab of Crop Improvement & Germplasm EnhancementLanzhou, 730070, China
- College of Agronomy, Gansu Agricultural UniversityLanzhou, 730070, China
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Abstract
Patterns of evolution in immune defense genes help to understand the evolutionary dynamics between hosts and pathogens. Multiple insect genomes have been sequenced, with many of them having annotated immune genes, which paves the way for a comparative genomic analysis of insect immunity. In this review, I summarize the current state of comparative and evolutionary genomics of insect innate immune defense. The focus is on the conserved and divergent components of immunity with an emphasis on gene family evolution and evolution at the sequence level; both population genetics and molecular evolution frameworks are considered.
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Arango-Velez A, González LMG, Meents MJ, El Kayal W, Cooke BJ, Linsky J, Lusebrink I, Cooke JEK. Influence of water deficit on the molecular responses of Pinus contorta × Pinus banksiana mature trees to infection by the mountain pine beetle fungal associate, Grosmannia clavigera. TREE PHYSIOLOGY 2014; 34:1220-39. [PMID: 24319029 PMCID: PMC4277265 DOI: 10.1093/treephys/tpt101] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 10/08/2013] [Indexed: 05/14/2023]
Abstract
Conifers exhibit a number of constitutive and induced mechanisms to defend against attack by pests and pathogens such as mountain pine beetle (Dendroctonus ponderosae Hopkins) and their fungal associates. Ecological studies have demonstrated that stressed trees are more susceptible to attack by mountain pine beetle than their healthy counterparts. In this study, we tested the hypothesis that water deficit affects constitutive and induced responses of mature lodgepole pine × jack pine hybrids (Pinus contorta Dougl. ex Loud. var. latifolia Engelm. ex S. Wats. × Pinus banksiana Lamb.) to inoculation with the mountain pine beetle fungal associate Grosmannia clavigera (Robinson-Jeffrey and Davidson) Zipfel, de Beer and Wingfield. The degree of stress induced by the imposed water-deficit treatment was sufficient to reduce photosynthesis. Grosmannia clavigera-induced lesions exhibited significantly reduced dimensions in water-deficit trees relative to well-watered trees at 5 weeks after inoculation. Treatment-associated cellular-level changes in secondary phloem were also observed. Quantitative RT-PCR was used to analyze transcript abundance profiles of 18 genes belonging to four families classically associated with biotic and abiotic stress responses: aquaporins (AQPs), dehydration-responsive element binding (DREB), terpene synthases (TPSs) and chitinases (CHIs). Transcript abundance profiles of a TIP2 AQP and a TINY-like DREB decreased significantly in fungus-inoculated trees, but not in response to water deficit. One TPS, Pcb(+)-3-carene synthase, and the Class II CHIs PcbCHI2.1 and PcbCHI2.2 showed increased expression under water-deficit conditions in the absence of fungal inoculation, while another TPS, Pcb(E)-β-farnesene synthase-like, and two CHIs, PcbCHI1.1 and PcbCHI4.1, showed attenuated expression under water-deficit conditions in the presence of fungal inoculation. The effects were observed both locally and systemically. These results demonstrate that both constitutive and induced carbon- and nitrogen-based defenses are affected by water deficit, suggesting potential consequences for mountain pine beetle dynamics, particularly in novel environments.
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Affiliation(s)
- Adriana Arango-Velez
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Leonardo M Galindo González
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Miranda J Meents
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Walid El Kayal
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Barry J Cooke
- Natural Resources Canada, Canadian Forest Service, Northern Forestry Centre, Edmonton, AB, Canada T6H 3S5
| | - Jean Linsky
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
| | - Inka Lusebrink
- Department of Renewable Resources, University of Alberta, Edmonton, AB, Canada T6E 2E3
| | - Janice E K Cooke
- Department of Biological Sciences, University of Alberta, CW405 Biological Sciences Building, Edmonton, AB, Canada T6G 2E9
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The complex jujube genome provides insights into fruit tree biology. Nat Commun 2014; 5:5315. [PMID: 25350882 PMCID: PMC4220462 DOI: 10.1038/ncomms6315] [Citation(s) in RCA: 153] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2014] [Accepted: 09/18/2014] [Indexed: 12/20/2022] Open
Abstract
The jujube (Ziziphus jujuba Mill.), a member of family Rhamnaceae, is a major
dry fruit and a traditional herbal medicine for more than one billion people. Here
we present a high-quality sequence for the complex jujube genome, the first genome
sequence of Rhamnaceae, using an integrated strategy. The final assembly spans
437.65 Mb (98.6% of the estimated) with 321.45 Mb anchored to
the 12 pseudo-chromosomes and contains 32,808 genes. The jujube genome has undergone
frequent inter-chromosome fusions and segmental duplications, but no recent
whole-genome duplication. Further analyses of the jujube-specific genes and
transcriptome data from 15 tissues reveal the molecular mechanisms underlying some
specific properties of the jujube. Its high vitamin C content can be attributed to a
unique high level expression of genes involved in both biosynthesis and
regeneration. Our study provides insights into jujube-specific biology and valuable
genomic resources for the improvement of Rhamnaceae plants and other fruit
trees. The jujube is a major dry fruit crop in China and is commonly used for
medicinal purposes. Here the authors sequence the genome and transcriptome of the most
widely cultivated jujube cultivar, Dongzao, and highlight the genetic and molecular
basis of agronomically important jujube traits, such as vitamin C content.
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45
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Sahu SS, Weirick T, Kaundal R. Predicting genome-scale Arabidopsis-Pseudomonas syringae interactome using domain and interolog-based approaches. BMC Bioinformatics 2014; 15 Suppl 11:S13. [PMID: 25350354 PMCID: PMC4251041 DOI: 10.1186/1471-2105-15-s11-s13] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Every year pathogenic organisms cause billions of dollars' worth damage to crops and livestock. In agriculture, study of plant-microbe interactions is demanding a special attention to develop management strategies for the destructive pathogen induced diseases that cause huge crop losses every year worldwide. Pseudomonas syringae is a major bacterial leaf pathogen that causes diseases in a wide range of plant species. Among its various strains, pathovar tomato strain DC3000 (PstDC3000) is asserted to infect the plant host Arabidopsis thaliana and thus, has been accepted as a model system for experimental characterization of the molecular dynamics of plant-pathogen interactions. Protein-protein interactions (PPIs) play a critical role in initiating pathogenesis and maintaining infection. Understanding the PPI network between a host and pathogen is a critical step for studying the molecular basis of pathogenesis. The experimental study of PPIs at a large scale is very scarce and also the high throughput experimental results show high false positive rate. Hence, there is a need for developing efficient computational models to predict the interaction between host and pathogen in a genome scale, and find novel candidate effectors and/or their targets. RESULTS In this study, we used two computational approaches, the interolog and the domain-based to predict the interactions between Arabidopsis and PstDC3000 in genome scale. The interolog method relies on protein sequence similarity to conduct the PPI prediction. A Pseudomonas protein and an Arabidopsis protein are predicted to interact with each other if an experimentally verified interaction exists between their respective homologous proteins in another organism. The domain-based method uses domain interaction information, which is derived from known protein 3D structures, to infer the potential PPIs. If a Pseudomonas and an Arabidopsis protein contain an interacting domain pair, one can expect the two proteins to interact with each other. The interolog-based method predicts ~0.79M PPIs involving around 7700 Arabidopsis and 1068 Pseudomonas proteins in the full genome. The domain-based method predicts 85650 PPIs comprising 11432 Arabidopsis and 887 Pseudomonas proteins. Further, around 11000 PPIs have been identified as interacting from both the methods as a consensus. CONCLUSION The present work predicts the protein-protein interaction network between Arabidopsis thaliana and Pseudomonas syringae pv. tomato DC3000 in a genome wide scale with a high confidence. Although the predicted PPIs may contain some false positives, the computational methods provide reasonable amount of interactions which can be further validated by high throughput experiments. This can be a useful resource to the plant community to characterize the host-pathogen interaction in Arabidopsis and Pseudomonas system. Further, these prediction models can be applied to the agriculturally relevant crops.
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Affiliation(s)
- Sitanshu S Sahu
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity (NIMFFAB), Oklahoma State University, Stillwater, 74078, USA
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, 74078, USA
| | - Tyler Weirick
- National Institute for Microbial Forensics & Food and Agricultural Biosecurity (NIMFFAB), Oklahoma State University, Stillwater, 74078, USA
- Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, 74078, USA
| | - Rakesh Kaundal
- Bioinformatics Facility, Department of Botany & Plant Sciences, Institute for Integrative Genome Biology (IIGB), University of California, Riverside, California, 92521, USA
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Rech GE, Sanz-Martín JM, Anisimova M, Sukno SA, Thon MR. Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus. Genome Biol Evol 2014; 6:2368-79. [PMID: 25193312 PMCID: PMC4202328 DOI: 10.1093/gbe/evu192] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2014] [Indexed: 12/20/2022] Open
Abstract
Natural selection leaves imprints on DNA, offering the opportunity to identify functionally important regions of the genome. Identifying the genomic regions affected by natural selection within pathogens can aid in the pursuit of effective strategies to control diseases. In this study, we analyzed genome-wide patterns of selection acting on different classes of sequences in a worldwide sample of eight strains of the model plant-pathogenic fungus Colletotrichum graminicola. We found evidence of selective sweeps, balancing selection, and positive selection affecting both protein-coding and noncoding DNA of pathogenicity-related sequences. Genes encoding putative effector proteins and secondary metabolite biosynthetic enzymes show evidence of positive selection acting on the coding sequence, consistent with an Arms Race model of evolution. The 5' untranslated regions (UTRs) of genes coding for effector proteins and genes upregulated during infection show an excess of high-frequency polymorphisms likely the consequence of balancing selection and consistent with the Red Queen hypothesis of evolution acting on these putative regulatory sequences. Based on the findings of this work, we propose that even though adaptive substitutions on coding sequences are important for proteins that interact directly with the host, polymorphisms in the regulatory sequences may confer flexibility of gene expression in the virulence processes of this important plant pathogen.
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Affiliation(s)
- Gabriel E Rech
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Villamayor, Spain
| | - José M Sanz-Martín
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Villamayor, Spain
| | - Maria Anisimova
- Computer Science Department, ETH Zürich, Universitätsstrasse 6, Zürich, Switzerland Institute of Applied Simulation, Zürich University of Applied Sciences (ZHAW), Wädenswil, Switzerland
| | - Serenella A Sukno
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Villamayor, Spain
| | - Michael R Thon
- Departamento de Microbiología y Genética, Instituto Hispano-Luso de Investigaciones Agrarias (CIALE), Universidad de Salamanca, Villamayor, Spain
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Thavamanikumar S, Southerton S, Thumma B. RNA-Seq using two populations reveals genes and alleles controlling wood traits and growth in Eucalyptus nitens. PLoS One 2014; 9:e101104. [PMID: 24967893 PMCID: PMC4072731 DOI: 10.1371/journal.pone.0101104] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 06/02/2014] [Indexed: 11/17/2022] Open
Abstract
Eucalyptus nitens is a perennial forest tree species grown mainly for kraft pulp production in many parts of the world. Kraft pulp yield (KPY) is a key determinant of plantation profitability and increasing the KPY of trees grown in plantations is a major breeding objective. To speed up the breeding process, molecular markers that can predict KPY are desirable. To achieve this goal, we carried out RNA-Seq studies on trees at extremes of KPY in two different trials to identify genes and alleles whose expression correlated with KPY. KPY is positively correlated with growth measured as diameter at breast height (DBH) in both trials. In total, six RNA bulks from two treatments were sequenced on an Illumina HiSeq platform. At 5% false discovery rate level, 3953 transcripts showed differential expression in the same direction in both trials; 2551 (65%) were down-regulated and 1402 (35%) were up-regulated in low KPY samples. The genes up-regulated in low KPY trees were largely involved in biotic and abiotic stress response reflecting the low growth among low KPY trees. Genes down-regulated in low KPY trees mainly belonged to gene categories involved in wood formation and growth. Differential allelic expression was observed in 2103 SNPs (in 1068 genes) and of these 640 SNPs (30%) occurred in 313 unique genes that were also differentially expressed. These SNPs may represent the cis-acting regulatory variants that influence total gene expression. In addition we also identified 196 genes which had Ka/Ks ratios greater than 1.5, suggesting that these genes are under positive selection. Candidate genes and alleles identified in this study will provide a valuable resource for future association studies aimed at identifying molecular markers for KPY and growth.
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Affiliation(s)
- Saravanan Thavamanikumar
- Department of Forest and Ecosystem Science, University of Melbourne, Creswick, Victoria, Australia
| | | | - Bala Thumma
- CSIRO Plant Industry, Acton, ACT, Australia
- * E-mail:
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Detecting selection in the blue crab, Callinectes sapidus, using DNA sequence data from multiple nuclear protein-coding genes. PLoS One 2014; 9:e99081. [PMID: 24896825 PMCID: PMC4045945 DOI: 10.1371/journal.pone.0099081] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Accepted: 05/11/2014] [Indexed: 11/23/2022] Open
Abstract
The identification of genes involved in the adaptive evolution of non-model organisms with uncharacterized genomes constitutes a major challenge. This study employed a rigorous and targeted candidate gene approach to test for positive selection on protein-coding genes of the blue crab, Callinectes sapidus. Four genes with putative roles in physiological adaptation to environmental stress were chosen as candidates. A fifth gene not expected to play a role in environmental adaptation was used as a control. Large samples (n>800) of DNA sequences from C. sapidus were used in tests of selective neutrality based on sequence polymorphisms. In combination with these, sequences from the congener C. similis were used in neutrality tests based on interspecific divergence. In multiple tests, significant departures from neutral expectations and indicative of positive selection were found for the candidate gene trehalose 6-phosphate synthase (tps). These departures could not be explained by any of the historical population expansion or bottleneck scenarios that were evaluated in coalescent simulations. Evidence was also found for balancing selection at ATP-synthase subunit 9 (atps) using a maximum likelihood version of the Hudson, Kreitmen, and Aguadé test, and positive selection favoring amino acid replacements within ATP/ADP translocase (ant) was detected using the McDonald-Kreitman test. In contrast, test statistics for the control gene, ribosomal protein L12 (rpl), which presumably has experienced the same demographic effects as the candidate loci, were not significantly different from neutral expectations and could readily be explained by demographic effects. Together, these findings demonstrate the utility of the candidate gene approach for investigating adaptation at the molecular level in a marine invertebrate for which extensive genomic resources are not available.
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Tobias PA, Guest DI. Tree immunity: growing old without antibodies. TRENDS IN PLANT SCIENCE 2014; 19:367-70. [PMID: 24556378 DOI: 10.1016/j.tplants.2014.01.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 01/18/2014] [Accepted: 01/21/2014] [Indexed: 05/04/2023]
Abstract
Perennial plants need to cope with changing environments and pathogens over their lifespan. Infections are compartmentalised by localised physiological responses, and multiple apical meristems enable repair and regrowth, but genes are another crucial component in the perception and response to pathogens. In this opinion article we suggest that the mechanism for dynamic pathogen-specific recognition in long-lived plants could be explained by extending our current understanding of plant defence genes. We propose that, in addition to physiological responses, tree defence uses a three-pronged genomic approach involving: (i) gene numbers, (ii) genomic architecture, and (iii) mutation loads accumulated over long lifespans.
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Affiliation(s)
- Peri A Tobias
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Biomedical Building C81, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW 2015, Australia.
| | - David I Guest
- Department of Plant and Food Sciences, Faculty of Agriculture and Environment, University of Sydney, Biomedical Building C81, 1 Central Avenue, Australian Technology Park, Eveleigh, NSW 2015, Australia
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Structure-based computational study of two disease resistance gene homologues (Hm1 and Hm2) in maize (Zea mays L.) with implications in plant-pathogen interactions. PLoS One 2014; 9:e97852. [PMID: 24847713 PMCID: PMC4029905 DOI: 10.1371/journal.pone.0097852] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2014] [Accepted: 04/25/2014] [Indexed: 11/30/2022] Open
Abstract
The NADPH-dependent HC-toxin reductases (HCTR1 and 2) encoded by enzymatic class of disease resistance homologous genes (Hm1 and Hm2) protect maize by detoxifying a cyclic tetrapeptide, HC-toxin, secreted by the fungus Cochliobolus carbonum race 1(CCR1). Unlike the other classes' resistance (R) genes, HCTR-mediated disease resistance is an inimitable mechanism where the avirulence (Avr) component from CCR1 is not involved in toxin degradation. In this study, we attempted to decipher cofactor (NADPH) recognition and mode of HC-toxin binding to HCTRs through molecular docking, molecular dynamics (MD) simulations and binding free energy calculation methods. The rationality and the stability of docked complexes were validated by 30-ns MD simulation. The binding free energy decomposition of enzyme-cofactor complex was calculated to find the driving force behind cofactor recognition. The overall binding free energies of HCTR1-NADPH and HCTR2-NADPH were found to be −616.989 and −16.9749 kJ mol−1 respectively. The binding free energy decomposition revealed that the binding of NADPH to the HCTR1 is mainly governed by van der Waals and nonpolar interactions, whereas electrostatic terms play dominant role in stabilizing the binding mode between HCTR2 and NADPH. Further, docking analysis of HC-toxin with HCTR-NADPH complexes showed a distinct mode of binding and the complexes were stabilized by a strong network of hydrogen bond and hydrophobic interactions. This study is the first in silico attempt to unravel the biophysical and biochemical basis of cofactor recognition in enzymatic class of R genes in cereal crop maize.
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