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Teyssier C, Rogier O, Claverol S, Gautier F, Lelu-Walter MA, Duruflé H. Comprehensive Organ-Specific Profiling of Douglas Fir ( Pseudotsuga menziesii) Proteome. Biomolecules 2023; 13:1400. [PMID: 37759800 PMCID: PMC10526743 DOI: 10.3390/biom13091400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/13/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
The Douglas fir (Pseudotsuga menziesii) is a conifer native to North America that has become increasingly popular in plantations in France due to its many advantages as timber: rapid growth, quality wood, and good adaptation to climate change. Tree genetic improvement programs require knowledge of a species' genetic structure and history and the development of genetic markers. The very slow progress in this field, for Douglas fir as well as the entire genus Pinus, can be explained using the very large size of their genomes, as well as by the presence of numerous highly repeated sequences. Proteomics, therefore, provides a powerful way to access genomic information of otherwise challenging species. Here, we present the first Douglas fir proteomes acquired using nLC-MS/MS from 12 different plant organs or tissues. We identified 3975 different proteins and quantified 3462 of them, then examined the distribution of specific proteins across plant organs/tissues and their implications in various molecular processes. As the first large proteomic study of a resinous tree species with organ-specific profiling, this short note provides an important foundation for future genomic annotations of conifers and other trees.
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Affiliation(s)
| | - Odile Rogier
- INRAE, ONF, BioForA, UMR 0588, 45075 Orleans, France
| | - Stéphane Claverol
- Plateforme de Protéomique, Université de Bordeaux, 33405 Bordeaux, France
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Ding X, Li Y, Zhang Y, Diao S, Luan Q, Jiang J. Genetic analysis and elite tree selection of the main resin components of slash pine. FRONTIERS IN PLANT SCIENCE 2023; 14:1079952. [PMID: 36818862 PMCID: PMC9930156 DOI: 10.3389/fpls.2023.1079952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 01/13/2023] [Indexed: 06/18/2023]
Abstract
Pine resin, as a natural material, has been widely used in food, pharmaceutical, and chemical industries. Slash pine (Pinus elliottii Engelm var. elliottii) is the primary tree species for resin tapping due to its high resin yield, low resin crystallization rate, and high turpentine content. Current researches focuse on the targeted improvement of several significant components to meet industrial needs rather than just resin yield. The objective of this study was to examine the genetic variation and correlation of genetic and phenotype for four main resin components (α pinene, β pinene, abietic acid, and levoprimaric acid) of 219 half-sib progenies from 59 families. The results showed that the levopimaric acid had the largest content (mean value = 21.63%), while the β pinene content had the largest variation coefficient (CV = 0.42). The α pinene content has the highest heritability (h2 = 0.67), while levopimaric acid has the lowest heritability (h2 = 0.51). There was a significant negative correlation between α pinene and the other three components and a significant positive correlation between β pinene and the two diterpenes. The family ranking and genetic gain suggested that it is possible to improve the contents of main resin components of slash pine through genetic breeding selection.
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Affiliation(s)
- Xianyin Ding
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Exotic Pine Cultivation Engineering Technology Research Center of National Forestry and Grassland Administration, Hangzhou, China
| | - Yanjie Li
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Yini Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
| | - Shu Diao
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Exotic Pine Cultivation Engineering Technology Research Center of National Forestry and Grassland Administration, Hangzhou, China
| | - Qifu Luan
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Exotic Pine Cultivation Engineering Technology Research Center of National Forestry and Grassland Administration, Hangzhou, China
| | - Jingmin Jiang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, China
- Exotic Pine Cultivation Engineering Technology Research Center of National Forestry and Grassland Administration, Hangzhou, China
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Chiu CC, Bohlmann J. Mountain Pine Beetle Epidemic: An Interplay of Terpenoids in Host Defense and Insect Pheromones. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:475-494. [PMID: 35130442 DOI: 10.1146/annurev-arplant-070921-103617] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The mountain pine beetle epidemic has highlighted the complex interactions of bark beetles with conifer host defenses. In these interactions, oleoresin terpenoids and volatiles, produced and released by the host tree, can be both harmful and beneficial to the beetle's success in colonizing a tree and completing its life cycle. The insect spends almost its entire life, from egg to adult, within the bark and phloem of a pine host, exposed to large quantities of complex mixtures of oleoresin terpenoids. Conifer oleoresin comprises mostly monoterpenes and diterpene resin acids as well as many different sesquiterpenes. It functions as a major chemical and physical defense system. However, the insect has evolved host colonization behavior and enzymes for terpenoid metabolism and detoxification that allow it to overcome some of the terpenoid defenses and, importantly, to co-opt pine monoterpenes as cues for host search and as a precursor for its own pheromone system. The insect-associated microbiome also plays a role in the metabolism of conifer terpenoids.
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Affiliation(s)
- Christine C Chiu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada;
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada;
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Alicandri E, Covino S, Sebastiani B, Paolacci AR, Badiani M, Sorgonà A, Ciaffi M. Monoterpene Synthase Genes and Monoterpene Profiles in Pinus nigra subsp. laricio. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030449. [PMID: 35161430 PMCID: PMC8838282 DOI: 10.3390/plants11030449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 05/09/2023]
Abstract
In the present study, we carried out a quantitative analysis of the monoterpenes composition in different tissues of the non-model conifer Pinus nigra J.F. Arnold subsp. laricio Palib. ex Maire (P. laricio, in short). All the P. laricio tissues examined showed the presence of the same fourteen monoterpenes, among which the most abundant were β-phellandrene, α-pinene, and β-pinene, whose distribution was markedly tissue-specific. In parallel, from the same plant tissues, we isolated seven full-length cDNA transcripts coding for as many monoterpene synthases, each of which was found to be attributable to one of the seven phylogenetic groups in which the d1-clade of the canonical classification of plants' terpene synthases can be subdivided. The amino acid sequences deduced from the above cDNA transcripts allowed to predict their putative involvement in the biosynthesis of five of the monoterpenes identified. Transcripts profiling revealed a differential gene expression across the different tissues examined, and was found to be consistent with the corresponding metabolites profiles. The genomic organization of the seven isolated monoterpene synthase genes was also determined.
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Affiliation(s)
- Enrica Alicandri
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, I-89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Stefano Covino
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Bartolomeo Sebastiani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto, 8, I-06123 Perugia, Italy;
| | - Anna Rita Paolacci
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Maurizio Badiani
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, I-89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Agostino Sorgonà
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, I-89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Mario Ciaffi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c, I-01100 Viterbo, Italy; (S.C.); (A.R.P.)
- Correspondence: ; Tel.: +39-0761-357-424; Fax: +39-0761-357-389
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Alicandri E, Covino S, Sebastiani B, Paolacci AR, Badiani M, Manti F, Bonsignore CP, Sorgonà A, Ciaffi M. Diterpene Resin Acids and Olefins in Calabrian Pine ( Pinus nigra subsp. laricio (Poiret) Maire) Oleoresin: GC-MS Profiling of Major Diterpenoids in Different Plant Organs, Molecular Identification and Expression Analysis of Diterpene Synthase Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112391. [PMID: 34834754 PMCID: PMC8622628 DOI: 10.3390/plants10112391] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/28/2021] [Accepted: 11/04/2021] [Indexed: 05/04/2023]
Abstract
A quali-quantitative analysis of diterpenoid composition in tissues obtained from different organs of Pinus nigra subsp. laricio (Poiret) Maire (Calabrian pine) was carried out. Diterpene resin acids were the most abundant diterpenoids across all the examined tissues. The same nine diterpene resin acids were always found, with the abietane type prevailing on the pimarane type, although their quantitative distribution was found to be remarkably tissue-specific. The scrutiny of the available literature revealed species specificity as well. A phylogeny-based approach allowed us to isolate four cDNAs coding for diterpene synthases in Calabrian pine, each of which belonging to one of the four groups into which the d3 clade of the plants' terpene synthases family can be divided. The deduced amino acid sequences allowed predicting that both monofunctional and bifunctional diterpene synthases are involved in the biosynthesis of diterpene resin acids in Calabrian pine. Transcript profiling revealed differential expression across the different tissues and was found to be consistent with the corresponding diterpenoid profiles. The isolation of the complete genomic sequences and the determination of their exon/intron structures allowed us to place the diterpene synthase genes from Calabrian pine on the background of current ideas on the functional evolution of diterpene synthases in Gymnosperms.
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Affiliation(s)
- Enrica Alicandri
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Stefano Covino
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Bartolomeo Sebastiani
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 8, 06123 Perugia, Italy;
| | - Anna Rita Paolacci
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
| | - Maurizio Badiani
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Francesco Manti
- Dipartimento di Patrimonio, Architettura e Urbanistica, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy; (F.M.); (C.P.B.)
| | - Carmelo Peter Bonsignore
- Dipartimento di Patrimonio, Architettura e Urbanistica, Università Mediterranea di Reggio Calabria, Salita Melissari, 89124 Reggio Calabria, Italy; (F.M.); (C.P.B.)
| | - Agostino Sorgonà
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Loc. Feo di Vito, 89129 Reggio Calabria, Italy; (E.A.); (M.B.); (A.S.)
| | - Mario Ciaffi
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Via S. Camillo De Lellis, s.n.c., 01100 Viterbo, Italy; (S.C.); (A.R.P.)
- Correspondence: ; Tel.: +39-0761-357-424; Fax: +39-0761-357-389
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Lei D, Qiu Z, Qiao J, Zhao GR. Plasticity engineering of plant monoterpene synthases and application for microbial production of monoterpenoids. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:147. [PMID: 34193244 PMCID: PMC8247113 DOI: 10.1186/s13068-021-01998-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 06/18/2021] [Indexed: 05/17/2023]
Abstract
Plant monoterpenoids with structural diversities have extensive applications in food, cosmetics, pharmaceuticals, and biofuels. Due to the strong dependence on the geographical locations and seasonal annual growth of plants, agricultural production for monoterpenoids is less effective. Chemical synthesis is also uneconomic because of its high cost and pollution. Recently, emerging synthetic biology enables engineered microbes to possess great potential for the production of plant monoterpenoids. Both acyclic and cyclic monoterpenoids have been synthesized from fermentative sugars through heterologously reconstructing monoterpenoid biosynthetic pathways in microbes. Acting as catalytic templates, plant monoterpene synthases (MTPSs) take elaborate control of the monoterpenoids production. Most plant MTPSs have broad substrate or product properties, and show functional plasticity. Thus, the substrate selectivity, product outcomes, or enzymatic activities can be achieved by the active site mutations and domain swapping of plant MTPSs. This makes plasticity engineering a promising way to engineer MTPSs for efficient production of natural and non-natural monoterpenoids in microbial cell factories. Here, this review summarizes the key advances in plasticity engineering of plant MTPSs, including the fundamental aspects of functional plasticity, the utilization of natural and non-natural substrates, and the outcomes from product isomers to complexity-divergent monoterpenoids. Furthermore, the applications of plasticity engineering for improving monoterpenoids production in microbes are addressed.
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Affiliation(s)
- Dengwei Lei
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Zetian Qiu
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Jianjun Qiao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China
| | - Guang-Rong Zhao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
- SynBio Research Platform, Collaborative Innovation Centre of Chemical Science and Engineering (Tianjin), Tianjin University, Yaguan Road 135, Jinnan District, Tianjin, 300350, China.
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Xu J, Peng G, Xu J, Li Y, Tong L, Yang D. Probing of the plasticity of the active site in pinene synthase elucidates its potential evolutionary mechanism. PHYTOCHEMISTRY 2021; 181:112573. [PMID: 33142148 DOI: 10.1016/j.phytochem.2020.112573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/19/2020] [Accepted: 10/22/2020] [Indexed: 06/11/2023]
Abstract
Terpenes form a class of highly diverse natural products. The diversity of terpenes is created by terpene synthases. During the reaction, carbocation intermediates form and their rearrangement could lead to the formation of various products. Terpene synthases determine the final product profile by controlling the conformation of the intermediate or stabilizing the carbocation. Pinene synthase is a monoterpene synthase catalyzing the cyclization of geranyl pyrophosphate (GPP) to form pinene. Our study suggests that by mutating the aromatic residue F482 to Ala, Val, Ile and Thr, the enzyme can be converted to sabinene synthase, with more than 90% of its total terpene products becoming sabinene, which indicates the aromaticity of this residue is essential for stabilizing the pinyl carbocation. We also identified a mutation S491A that could cause an about 29% increase in the overall activity of the enzyme without altering its produce selectivity. Molecular dynamic simulation indicates this mutation could decrease the flexibility of the enzyme when it forms a complex with the pinyl carbocation. Our study suggests the active pocket of pinene synthase has a certain level of plasticity, making it relatively easy to change the product selectivity or overall activity. This property could have an important implication in the evolution of terpene synthases and thereby terpene diversity, as by changing a few residues an enzyme could synthesize a completely different terpene product in a significant amount, which allows selection to take place.
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Affiliation(s)
- Jingwei Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Guanzu Peng
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jinkun Xu
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yi Li
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Li Tong
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Dong Yang
- Gene Engineering and Biotechnology Beijing Key Laboratory, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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Liu L, Wang Z, Su Y, Wang T. Characterization and Analysis of the Full-Length Transcriptomes of Multiple Organs in Pseudotaxus chienii (W.C.Cheng) W.C.Cheng. Int J Mol Sci 2020; 21:ijms21124305. [PMID: 32560294 PMCID: PMC7352595 DOI: 10.3390/ijms21124305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 06/08/2020] [Accepted: 06/12/2020] [Indexed: 01/06/2023] Open
Abstract
Pseudotaxus chienii, a rare tertiary relict species with economic and ecological value, is a representative of the monotypic genus Pseudotaxus that is endemic to China. P. chienii can adapt well to habitat isolation and ecological heterogeneity under a variety of climate and soil conditions, and is able to survive in harsh environments. However, little is known about the molecular and genetic resources of this long-lived conifer. Herein, we sequenced the transcriptomes of four organs of P. chienii using the PacBio Isoform Sequencing and Illumina RNA Sequencing platforms. Based on the PacBio Iso-Seq data, we obtained 44,896, 58,082, 50,485, and 67,638 full-length unigenes from the root, stem, leaf, and strobilus, respectively, with a mean length of 2692 bp, and a mean N50 length of 3010.75 bp. We then comprehensively annotated these unigenes. The number of organ-specific expressed unigenes ranged from 4393 in leaf to 9124 in strobilus, suggesting their special roles in physiological processes, organ development, and adaptability in the different four organs. A total of 16,562 differentially expressed genes (DEGs) were identified among the four organs and clustered into six subclusters. The gene families related to biotic/abiotic factors, including the TPS, CYP450, and HSP families, were characterized. The expression levels of most DEGs in the phenylpropanoid biosynthesis pathway and plant–pathogen interactions were higher in the root than in the three other organs, suggesting that root constitutes the main organ of defensive compound synthesis and accumulation and has a stronger ability to respond to stress. The sequences were analyzed to predict transcription factors, long non-coding RNAs, and alternative splicing events. The expression levels of most DEGs of C2H2, C3H, bHLH, and bZIP families in the root and stem were higher than those in the leaf and strobilus, indicating that these TFs may play a crucial role in the survival of the root and stem. These results comprise the first comprehensive gene expression profiles obtained for different organs of P. chienii. Our findings will facilitate further studies on the functional genomics, adaptive evolution, and phylogeny of P. chienii, and lay the foundation for the development of conservation strategies for this endangered conifer.
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Affiliation(s)
- Li Liu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.L.); (Z.W.)
| | - Zhen Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.L.); (Z.W.)
| | - Yingjuan Su
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China; (L.L.); (Z.W.)
- Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
- Correspondence: (Y.S.); (T.W.); Tel.: +86-020-84111939 (Y.S.); +86-020-85280185 (T.W.)
| | - Ting Wang
- College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- Correspondence: (Y.S.); (T.W.); Tel.: +86-020-84111939 (Y.S.); +86-020-85280185 (T.W.)
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On the Evolution and Functional Diversity of Terpene Synthases in the Pinus Species: A Review. J Mol Evol 2020; 88:253-283. [PMID: 32036402 DOI: 10.1007/s00239-020-09930-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/17/2020] [Indexed: 02/02/2023]
Abstract
In the biosynthesis of terpenoids, the ample catalytic versatility of terpene synthases (TPS) allows the formation of thousands of different molecules. A steadily increasing number of sequenced plant genomes invariably show that the TPS gene family is medium to large in size, comprising from 30 to 100 functional members. In conifers, TPSs belonging to the gymnosperm-specific TPS-d subfamily produce a complex mixture of mono-, sesqui-, and diterpenoid specialized metabolites, which are found in volatile emissions and oleoresin secretions. Such substances are involved in the defence against pathogens and herbivores and can help to protect against abiotic stress. Oleoresin terpenoids can be also profitably used in a number of different fields, from traditional and modern medicine to fine chemicals, fragrances, and flavours, and, in the last years, in biorefinery too. In the present work, after summarizing the current views on the biosynthesis and biological functions of terpenoids, recent advances on the evolution and functional diversification of plant TPSs are reviewed, with a focus on gymnosperms. In such context, an extensive characterization and phylogeny of all the known TPSs from different Pinus species is reported, which, for such genus, can be seen as the first effort to explore the evolutionary history of the large family of TPS genes involved in specialized metabolism. Finally, an approach is described in which the phylogeny of TPSs in Pinus spp. has been exploited to isolate for the first time mono-TPS sequences from Pinus nigra subsp. laricio, an ecologically important endemic pine in the Mediterranean area.
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De La Torre AR, Piot A, Liu B, Wilhite B, Weiss M, Porth I. Functional and morphological evolution in gymnosperms: A portrait of implicated gene families. Evol Appl 2020; 13:210-227. [PMID: 31892953 PMCID: PMC6935586 DOI: 10.1111/eva.12839] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 04/25/2019] [Accepted: 07/02/2019] [Indexed: 12/12/2022] Open
Abstract
Gymnosperms diverged from their sister plant clade of flowering plants 300 Mya. Morphological and functional divergence between the two major seed plant clades involved significant changes in their reproductive biology, water-conducting systems, secondary metabolism, stress defense mechanisms, and small RNA-mediated epigenetic silencing. The relatively recent sequencing of several gymnosperm genomes and the development of new genomic resources have enabled whole-genome comparisons within gymnosperms, and between angiosperms and gymnosperms. In this paper, we aim to understand how genes and gene families have contributed to the major functional and morphological differences in gymnosperms, and how this information can be used for applied breeding and biotechnology. In addition, we have analyzed the angiosperm versus gymnosperm evolution of the pleiotropic drug resistance (PDR) gene family with a wide range of functionalities in plants' interaction with their environment including defense mechanisms. Some of the genes reviewed here are newly studied members of gene families that hold potential for biotechnological applications related to commercial and pharmacological value. Some members of conifer gene families can also be exploited for their potential in phytoremediation applications.
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Affiliation(s)
| | - Anthony Piot
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
| | - Bobin Liu
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
- College of ForestryFujian Agricultural and Forestry UniversityFuzhouFujianChina
| | | | - Matthew Weiss
- School of ForestryNorthern Arizona UniversityFlagstaffAZUSA
| | - Ilga Porth
- Department of Wood and Forest SciencesLaval UniversityQuebec CityQuebecCanada
- Institute for System and Integrated Biology (IBIS)Laval UniversityQuebec CityQuebecCanada
- Centre for Forest Research (CEF)Laval UniversityQuebec CityQuebecCanada
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Cullingham CI, Peery RM, Fortier CE, Mahon EL, Cooke JEK, Coltman DW. Linking genotype to phenotype to identify genetic variation relating to host susceptibility in the mountain pine beetle system. Evol Appl 2020; 13:48-61. [PMID: 31892943 PMCID: PMC6935584 DOI: 10.1111/eva.12773] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 01/09/2019] [Accepted: 01/13/2019] [Indexed: 12/24/2022] Open
Abstract
Identifying genetic variants responsible for phenotypic variation under selective pressure has the potential to enable productive gains in natural resource conservation and management. Despite this potential, identifying adaptive candidate loci is not trivial, and linking genotype to phenotype is a major challenge in contemporary genetics. Many of the population genetic approaches commonly used to identify adaptive candidates will simultaneously detect false positives, particularly in nonmodel species, where experimental evidence is seldom provided for putative roles of the adaptive candidates identified by outlier approaches. In this study, we use outcomes from population genetics, phenotype association, and gene expression analyses as multiple lines of evidence to validate candidate genes. Using lodgepole and jack pine as our nonmodel study species, we analyzed 17 adaptive candidate loci together with 78 putatively neutral loci at 58 locations across Canada (N > 800) to determine whether relationships could be established between these candidate loci and phenotype related to mountain pine beetle susceptibility. We identified two candidate loci that were significant across all population genetic tests, and demonstrated significant changes in transcript abundance in trees subjected to wounding or inoculation with the mountain pine beetle fungal associate Grosmannia clavigera. Both candidates are involved in central physiological processes that are likely to be invoked in a trees response to stress. One of these two candidate loci showed a significant association with mountain pine beetle attack status in lodgepole pine. The spatial distribution of the attack-associated allele further coincides with other indicators of susceptibility in lodgepole pine. These analyses, in which population genetics was combined with laboratory and field experimental validation approaches, represent first steps toward linking genetic variation to the phenotype of mountain pine beetle susceptibility in lodgepole and jack pine, and provide a roadmap for more comprehensive analyses.
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Affiliation(s)
| | - Rhiannon M. Peery
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Colleen E. Fortier
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - Elizabeth L. Mahon
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
- Department of Wood ScienceUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Janice E. K. Cooke
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
| | - David W. Coltman
- Department of Biological SciencesUniversity of AlbertaEdmontonAlbertaCanada
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12
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Mukrimin M, Kovalchuk A, Ghimire RP, Kivimäenpää M, Sun H, Holopainen JK, Asiegbu FO. Evaluation of potential genetic and chemical markers for Scots pine tolerance against Heterobasidion annosum infection. PLANTA 2019; 250:1881-1895. [PMID: 31485774 DOI: 10.1007/s00425-019-03270-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/27/2019] [Indexed: 05/12/2023]
Abstract
Two terpene compounds and four genes were identified as potential biomarkers for further evaluation for Scots pine susceptibility or tolerance against Heterobasidion annosum. Scots pine (Pinus sylvestris) is one of the main sources of timber in the boreal zone of Eurasia. Commercial pine plantations are vulnerable to root and butt rot disease caused by the fungus Heterobasidion annosum. The pathogen affects host growth rate, causes higher mortality and decreases in timber quality, resulting in considerable economic losses to forest owners. Genetic and biochemical factors contributing to Scots pine tolerance against H. annosum infection are not well understood. We assessed the predictive values of a set of potential genetic and chemical markers in a field experiment. We determined the expression levels of 25 genes and the concentrations of 36 terpenoid compounds in needles of 16 Scots pine trees randomly selected from a natural population prior to artificial infection. Stems of the same trees were artificially inoculated with H. annosum, and the length of necrotic lesions was documented 5 months post inoculation. Higher expression level of four genes included in our analysis and encoding predicted α-pinene synthase (two genes), geranyl diphosphate synthase (GPPS), and metacaspase 5 (MC5), could be associated with trees exhibiting increased levels of necrotic lesion formation in response to fungal inoculation. In contrast, concentrations of two terpenoid compounds, β-caryophyllene and α-humulene, showed significant negative correlations with the lesion size. Further studies with larger sample size will help to elucidate new biomarkers or clarify the potential of the evaluated markers for use in Scots pine disease resistance breeding programs.
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Affiliation(s)
- Mukrimin Mukrimin
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
- Department of Forestry, Faculty of Forestry, Hasanuddin University, Jln. Perintis Kemerdekaan Km. 10, 90245, Makassar, Indonesia
| | - Andriy Kovalchuk
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
| | - Rajendra P Ghimire
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, 70211, Kuopio, Finland
| | - Minna Kivimäenpää
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, 70211, Kuopio, Finland
| | - Hui Sun
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland
- Collaborative Innovation Center of Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jarmo K Holopainen
- Department of Environmental and Biological Sciences, Kuopio Campus, University of Eastern Finland (UEF), P.O. Box 1627, 70211, Kuopio, Finland
| | - Fred O Asiegbu
- Department of Forest Sciences, Faculty of Agriculture and Forestry, University of Helsinki, Latokartanonkaari 7, P.O. Box 27, 00014, Helsinki, Finland.
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13
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Celedon JM, Bohlmann J. Oleoresin defenses in conifers: chemical diversity, terpene synthases and limitations of oleoresin defense under climate change. THE NEW PHYTOLOGIST 2019; 224:1444-1463. [PMID: 31179548 DOI: 10.1111/nph.15984] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/16/2019] [Indexed: 05/20/2023]
Abstract
Conifers have evolved complex oleoresin terpene defenses against herbivores and pathogens. In co-evolved bark beetles, conifer terpenes also serve chemo-ecological functions as pheromone precursors, chemical barcodes for host identification, or nutrients for insect-associated microbiomes. We highlight the genomic, molecular and biochemical underpinnings of the large chemical space of conifer oleoresin terpenes and volatiles. Conifer terpenes are predominantly the products of the conifer terpene synthase (TPS) gene family. Terpene diversity is increased by cytochromes P450 of the CYP720B class. Many conifer TPS are multiproduct enzymes. Multisubstrate CYP720B enzymes catalyse multistep oxidations. We summarise known terpenoid gene functions in various different conifer species with reference to the annotated terpenoid gene space in a spruce genome. Overall, biosynthesis of terpene diversity in conifers is achieved through a system of biochemical radiation and metabolic grids. Expression of TPS and CYP720B genes can be specific to individual cell types of constitutive or traumatic resin duct systems. Induced terpenoid transcriptomes in resin duct cells lead to dynamic changes of terpene composition and quantity to fend off herbivores and pathogens. While terpenoid defenses have contributed much to the evolutionary success of conifers, under new conditions of climate change, these defences may become inconsequential against range-expanding forest pests.
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Affiliation(s)
- Jose M Celedon
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, V6T 1Z4, Canada
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Functions of mountain pine beetle cytochromes P450 CYP6DJ1, CYP6BW1 and CYP6BW3 in the oxidation of pine monoterpenes and diterpene resin acids. PLoS One 2019; 14:e0216753. [PMID: 31071168 PMCID: PMC6508646 DOI: 10.1371/journal.pone.0216753] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 04/26/2019] [Indexed: 01/17/2023] Open
Abstract
The mountain pine beetle (MPB; Dendroctonus ponderosae) is a forest insect pest that attacks several different pine (Pinus) species in its native range of distribution in western North America. MPB are exposed for most of their life cycle to the chemical defenses of their hosts. These defenses are dominated by oleoresin secretions containing mostly various monoterpenes and diterpene resin acids (DRAs). Cytochrome P450 enzymes (P450s) of the MPB are thought to be involved in the metabolism of at least some of these defense compounds. Here we describe the cloning and characterization of three MPB P450s, CYP6DJ1, CYP6BW1 and CYP6BW3, and their functions in the oxidation of various monoterpenes and diterpene resin acids. CYP6DJ1 oxidizes the monoterpenes (+)-(4R)-limonene, (-)-(4S)-limonene and terpinolene and produces (4R,8R)-limonene-8,9-epoxide, (4R,8S)-limonene-8,9-epoxide, (4S,8S)-limonene-8,9-epoxide, (4S,8R)-limonene-8,9-epoxide, perilla alcohol and several unidentified oxidized compounds. These products of CYP6DJ1 were also identified in extracts of MPB treated with the same monoterpenes. CYP6BW1 and CYP6BW3 both oxidize the DRAs abietic acid, dehydroabietic acid, neoabietic acid, levopimaric acid, palustric acid, and isopimaric acid, producing hydroxylated and epoxidized DRAs. CYP6DJ1, CYP6BW1 and CYP6BW3 appear to contribute to the metabolism of oleoresin terpenes as part of the MPB's ability to cope with host defenses.
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15
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Chiu CC, Keeling CI, Bohlmann J. The cytochrome P450 CYP6DE1 catalyzes the conversion of α-pinene into the mountain pine beetle aggregation pheromone trans-verbenol. Sci Rep 2019; 9:1477. [PMID: 30728428 PMCID: PMC6365528 DOI: 10.1038/s41598-018-38047-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 12/19/2018] [Indexed: 12/12/2022] Open
Abstract
The recent outbreak of the mountain pine beetle (Dendroctonus ponderosae; MPB) has affected over 20 M hectares of pine forests in western North America. During the colonization of host trees, female MPB release the aggregation pheromone (-)-trans-verbenol. (-)-trans-Verbenol is thought to be produced from the pine defense compound (-)-α-pinene by cytochrome P450 (P450) dependent hydroxylation. MPB may also use P450s for the detoxification of other monoterpenes of the pine defense system. Here we describe the functional characterization of MPB CYP6DE1. CYP6DE1, but not the closely related CYP6DE2, used the bicyclic monoterpenes (-)-α-pinene, (+)-α-pinene, (-)-β-pinene, (+)-β-pinene and (+)-3-carene as substrates. CYP6DE1 was not active with other monoterpenes or diterpene resin acids that were tested as substrates. trans-Verbenol is the major product of CYP6DE1 activity with (-)-α-pinene or (+)-α-pinene as substrates. When tested with blends of different ratios of (-)-α-pinene and (+)-α-pinene, CYP6DE1 produced trans-verbenol with an enantiomeric profile that was similar to that produced by female MPB exposed to the α-pinene enantiomers.
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Affiliation(s)
- Christine C Chiu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C., V6T 1Z4, Canada.,Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, B.C., V6T 1Z4, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C., V6T 1Z4, Canada.,Laurentian Forestry Centre, Canadian Forest Service, Natural Resources Canada, 1055 rue du P.E.P.S., P.O. Box 10380, Stn. Sainte-Foy, Québec, QC, G1V 4C7, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C., V6T 1Z4, Canada. .,Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, B.C., V6T 1Z4, Canada.
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16
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Ryu M, Mishra RC, Jeon J, Lee SK, Bae H. Drought-induced susceptibility for Cenangium ferruginosum leads to progression of Cenangium-dieback disease in Pinus koraiensis. Sci Rep 2018; 8:16368. [PMID: 30401938 PMCID: PMC6219526 DOI: 10.1038/s41598-018-34318-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 10/15/2018] [Indexed: 11/09/2022] Open
Abstract
Recently, the occurrence of "Cenangium-dieback" has been frequent and devastating. Cenangium-dieback is caused by an endophytic fungus Cenangium ferruginosum in stressed pine trees. Progression of the disease in terms of molecular interaction between host and pathogen is not well studied and there is a need to develop preventive strategies. Thus, we simulated disease conditions and studied the associated transcriptomics, metabolomics, and hormonal changes. Pinus koraiensis seedlings inoculated with C. ferruginosum were analyzed both under drought and well-watered conditions. Transcriptomic analysis suggested decreased expression of defense-related genes in C. ferruginosum-infected seedlings experiencing water-deficit. Further, metabolomic analysis indicated a decrease in the key antimicrobial terpenoids, flavonoids, and phenolic acids. Hormonal analysis revealed a drought-induced accumulation of abscisic acid and a corresponding decline in the defense-associated jasmonic acid levels. Pathogen-associated changes were also studied by treating C. ferruginosum with metabolic extracts from pine seedlings (with and without drought) and polyethylene glycol to simulate the effects of direct drought. From RNA sequencing and metabolomic analysis it was determined that drought did not directly induce pathogenicity of C. ferruginosum. Collectively, we propose that drought weakens pine immunity, which facilitates increased C. ferruginosum growth and results in conversion of the endophyte into the phytopathogen causing dieback.
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Affiliation(s)
- Minji Ryu
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Ratnesh Chandra Mishra
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea
| | - Sun Keun Lee
- Division of Forest Insect Pests and Diseases, National Institute of Forest Science, Seoul, 02455, Republic of Korea
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Republic of Korea.
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17
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Formighieri C, Melis A. Cyanobacterial production of plant essential oils. PLANTA 2018; 248:933-946. [PMID: 29974209 DOI: 10.1007/s00425-018-2948-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/25/2018] [Indexed: 05/12/2023]
Abstract
Synechocystis (a cyanobacterium) was employed as an alternative host for the production of plant essential oil constituents. β-Phellandrene synthase (PHLS) genes from different plants, when expressed in Synechocystis, enabled synthesis of variable monoterpene hydrocarbon blends, converting Synechocystis into a cell factory that photosynthesized and released useful products. Monoterpene synthases are secondary metabolism enzymes that catalyze the generation of essential oil constituents in terrestrial plants. Essential oils, including monoterpene hydrocarbons, are of interest for their commercial application and value. Therefore, heterologous expression of monoterpene synthases for high-capacity essential oil production in photosynthetic microorganism transformants is of current interest. In the present work, the cyanobacterium Synechocystsis PCC 6803 was employed as an alternative host for the production of plant essential oil constituents. As a case study, β-phellandrene synthase (PHLS) genes from different plants were heterologously expressed in Synechocystis. Genomic integration of individual PHLS-encoding sequences endowed Synechocystis with constitutive monoterpene hydrocarbons generation, occurring concomitant with photosynthesis and cell growth. Specifically, the β-phellandrene synthase from Lavandula angustifolia (lavender), Solanum lycopersicum (tomato), Pinus banksiana (pine), Picea sitchensis (Sitka spruce) and Abies grandis (grand fir) were active in Synechocystis transformants but, instead of a single product, they generated a blend of terpene hydrocarbons comprising β-phellandrene, α-phellandrene, β-myrcene, β-pinene, and δ-carene with variable percentage ratios ranging from < 10 to > 90% in different product combinations and proportions. Our results suggested that PHLS enzyme conformation and function depends on the cytosolic environment in which they reside, with the biochemical properties of the latter causing catalytic deviations from the products naturally observed in the corresponding gene-encoding plants, giving rise to the terpene hydrocarbon blends described in this work. These findings may have commercial application in the generation of designer essential oil blends and will further assist the development of heterologous cyanobacterial platforms for the generation of desired monoterpene hydrocarbon products.
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Affiliation(s)
- Cinzia Formighieri
- Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Anastasios Melis
- Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA.
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18
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Cytochromes P450 Preferentially Expressed in Antennae of the Mountain Pine Beetle. J Chem Ecol 2018; 45:178-186. [DOI: 10.1007/s10886-018-0999-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Revised: 05/25/2018] [Accepted: 07/18/2018] [Indexed: 01/14/2023]
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Priya P, Yadav A, Chand J, Yadav G. Terzyme: a tool for identification and analysis of the plant terpenome. PLANT METHODS 2018; 14:4. [PMID: 29339971 PMCID: PMC5761147 DOI: 10.1186/s13007-017-0269-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 12/19/2017] [Indexed: 05/13/2023]
Abstract
BACKGROUND Terpenoid hydrocarbons represent the largest and most ancient group of phytochemicals, such that the entire chemical library of a plant is often referred to as its 'terpenome'. Besides having numerous pharmacological properties, terpenes contribute to the scent of the rose, the flavors of cinnamon and the yellow of sunflowers. Rapidly increasing -omics datasets provide an unprecedented opportunity for terpenome detection, paving the way for automated web resources dedicated to phytochemical predictions in genomic data. RESULTS We have developed Terzyme, a predictive algorithm for identification, classification and assignment of broad substrate unit to terpene synthase (TPS) and prenyl transferase (PT) enzymes, known to generate the enormous structural and functional diversity of terpenoid compounds across the plant kingdom. Terzyme uses sequence information, plant taxonomy and machine learning methods for predicting TPSs and PTs in genome and proteome datasets. We demonstrate a significant enrichment of the currently identified terpenome by running Terzyme on more than 40 plants. CONCLUSIONS Terzyme is the result of a rigorous analysis of evolutionary relationships between hundreds of characterized sequences of TPSs and PTs with known specificities, followed by analysis of genome-wide gene distribution patterns, ontology based clustering and optimization of various parameters for building accurate profile Hidden Markov Models. The predictive webserver and database is freely available at http://nipgr.res.in/terzyme.html and would serve as a useful tool for deciphering the species-specific phytochemical potential of plant genomes.
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Affiliation(s)
- Piyush Priya
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Archana Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Jyoti Chand
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067 India
- Department of Plant Sciences, University of Cambridge, Downing Site, Cambridge, CB2 3EA UK
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Chiu CC, Keeling CI, Bohlmann J. Toxicity of Pine Monoterpenes to Mountain Pine Beetle. Sci Rep 2017; 7:8858. [PMID: 28821756 PMCID: PMC5562797 DOI: 10.1038/s41598-017-08983-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 07/20/2017] [Indexed: 12/18/2022] Open
Abstract
The mountain pine beetle (Dendroctonus ponderosae; MPB) is an eruptive bark beetle species affecting pine forests of western North America. MPB are exposed to volatile monoterpenes, which are important host defense chemicals. We assessed the toxicity of the ten most abundant monoterpenes of lodgepole pine (Pinus contorta), a major host in the current MPB epidemic, against adult MPB from two locations in British Columbia, Canada. Monoterpenes were tested as individual volatiles and included (-)-β-phellandrene, (+)-3-carene, myrcene, terpinolene, and both enantiomers of α-pinene, β-pinene and limonene. Dose-mortality experiments identified (-)-limonene as the most toxic (LC50: 32 μL/L), and (-)-α-pinene (LC50: 290 μL/L) and terpinolene (LC50: >500 μL/L) as the least toxic. MPB body weight had a significant positive effect on the ability to survive most monoterpene volatiles, while sex did not have a significant effect with most monoterpenes. This study helps to quantitatively define the effects of individual monoterpenes towards MPB mortality, which is critical when assessing the variable monoterpene chemical defense profiles of its host species.
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Affiliation(s)
- Christine C Chiu
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C., V6T, 1Z4, Canada
- Botany Department, University of British Columbia, 6270 University Blvd, Vancouver, B.C., V6T 1Z4, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C., V6T, 1Z4, Canada
- Laurentian Forestry Centre, Natural Resources Canada, P.O. Box 10380, Stn. Sainte-Foy, 1055 du P.E.P.S., Quebec City, QC, G1V 4C7, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, B.C., V6T, 1Z4, Canada.
- Botany Department, University of British Columbia, 6270 University Blvd, Vancouver, B.C., V6T 1Z4, Canada.
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21
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Du J, Zhang Z, Zhang H, Junhong T. EST–SSR marker development and transcriptome sequencing analysis of different tissues of Korean pine ( Pinus koraiensis Sieb. et Zucc.). BIOTECHNOL BIOTEC EQ 2017. [DOI: 10.1080/13102818.2017.1331755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Jia Du
- Department of Environmental Engineering and Science, Hangzhou Dianzi University, Hangzhou, P. R. China
| | - Zhen Zhang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, P. R. China
| | - Hanguo Zhang
- School of Forestry, Northeast Forestry University, Harbin, P. R. China
| | - Tang Junhong
- Department of Environmental Engineering and Science, Hangzhou Dianzi University, Hangzhou, P. R. China
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22
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Burke JL, Bohlmann J, Carroll AL. Consequences of distributional asymmetry in a warming environment: invasion of novel forests by the mountain pine beetle. Ecosphere 2017. [DOI: 10.1002/ecs2.1778] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Jordan Lewis Burke
- Department of Forest and Conservation Sciences Faculty of Forestry The University of British Columbia 2424 Main Mall Vancouver British Columbia V6T 1Z4 Canada
| | - Joerg Bohlmann
- Department of Forest and Conservation Sciences Faculty of Forestry The University of British Columbia 2424 Main Mall Vancouver British Columbia V6T 1Z4 Canada
- Michael Smith Laboratories The University of British Columbia 2185 East Mall Vancouver British Columbia V6T 1Z4 Canada
| | - Allan L. Carroll
- Department of Forest and Conservation Sciences Faculty of Forestry The University of British Columbia 2424 Main Mall Vancouver British Columbia V6T 1Z4 Canada
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Liu ZK, Wen JB. Transcriptomic Analysis of Eucryptorrhynchus chinensis (Coleoptera: Curculionidae) Using 454 Pyrosequencing Technology. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew067. [PMID: 27620556 PMCID: PMC5019023 DOI: 10.1093/jisesa/iew067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Eucryptorrhynchus chinensis Olivier (Coleoptera: Curculionidae) is one of the most important pests of Ailanthus altissima; however, so far, no studies on the genome or transcriptome of E. chinensis have been reported. Using the Roche 454 FLX Titanium platform, an RNA pool obtained from E. chinensis eggs, larva, pupae, and adults was sequenced and assembled de novo to achieve maximum diversity of sampled transcripts. We obtained 1,441,137 (∼518 Mb) raw reads with an average length of 360 bp. After trimming, 89% qualified reads were produced and assembled into 35,509 isotigs with an average length of 440 bp, N50 of 1,048 bp, and 111,643 singletons. We generated 87,894 unigenes following a cluster analysis of the isotigs and singletons, and then functionally annotated the unigenes with gene descriptions. We obtained 23,363 GO assignments, and 12,724 unigenes were assigned to KOG. Based on these annotations, 294 biochemical pathways involved in growth, reproduction, and stress or immune responses were predicted. A total of 659,026 single nucleotide variants and 6,112 simple sequence repeats were detected. Our data provide comprehensive information on the sequence and possible functions of E. chinensis transcripts.
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Affiliation(s)
- Zhen-Kai Liu
- Beijing Key Laboratory of Forest Protection, College of Forestry, Beijing Forestry University, Beijing 100083, People's Republic of China (; )
| | - Jun-Bao Wen
- Beijing Key Laboratory of Forest Protection, College of Forestry, Beijing Forestry University, Beijing 100083, People's Republic of China (; )
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24
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de Lima JC, de Costa F, Füller TN, Rodrigues-Corrêa KCDS, Kerber MR, Lima MS, Fett JP, Fett-Neto AG. Reference Genes for qPCR Analysis in Resin-Tapped Adult Slash Pine As a Tool to Address the Molecular Basis of Commercial Resinosis. FRONTIERS IN PLANT SCIENCE 2016; 7:849. [PMID: 27379135 PMCID: PMC4909774 DOI: 10.3389/fpls.2016.00849] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 05/30/2016] [Indexed: 05/30/2023]
Abstract
Pine oleoresin is a major source of terpenes, consisting of turpentine (mono- and sesquiterpenes) and rosin (diterpenes) fractions. Higher oleoresin yields are of economic interest, since oleoresin derivatives make up a valuable source of materials for chemical industries. Oleoresin can be extracted from living trees, often by the bark streak method, in which bark removal is done periodically, followed by application of stimulant paste containing sulfuric acid and other chemicals on the freshly wounded exposed surface. To better understand the molecular basis of chemically-stimulated and wound induced oleoresin production, we evaluated the stability of 11 putative reference genes for the purpose of normalization in studying Pinus elliottii gene expression during oleoresinosis. Samples for RNA extraction were collected from field-grown adult trees under tapping operations using stimulant pastes with different compositions and at various time points after paste application. Statistical methods established by geNorm, NormFinder, and BestKeeper softwares were consistent in pointing as adequate reference genes HISTO3 and UBI. To confirm expression stability of the candidate reference genes, expression profiles of putative P. elliottii orthologs of resin biosynthesis-related genes encoding Pinus contorta β-pinene synthase [PcTPS-(-)β-pin1], P. contorta levopimaradiene/abietadiene synthase (PcLAS1), Pinus taeda α-pinene synthase [PtTPS-(+)αpin], and P. taeda α-farnesene synthase (PtαFS) were examined following stimulant paste application. Increased oleoresin yields observed in stimulated treatments using phytohormone-based pastes were consistent with higher expression of pinene synthases. Overall, the expression of all genes examined matched the expected profiles of oleoresin-related transcript changes reported for previously examined conifers.
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Affiliation(s)
- Júlio C. de Lima
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Fernanda de Costa
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Thanise N. Füller
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | | | - Magnus R. Kerber
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Mariano S. Lima
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Janette P. Fett
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
| | - Arthur G. Fett-Neto
- Plant Physiology Laboratory, Center for Biotechnology and Department of Botany, Federal University of Rio Grande do SulPorto Alegre, Brazil
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Geisler K, Jensen NB, Yuen MMS, Madilao L, Bohlmann J. Modularity of Conifer Diterpene Resin Acid Biosynthesis: P450 Enzymes of Different CYP720B Clades Use Alternative Substrates and Converge on the Same Products. PLANT PHYSIOLOGY 2016; 171:152-64. [PMID: 26936895 PMCID: PMC4854711 DOI: 10.1104/pp.16.00180] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/01/2016] [Indexed: 05/06/2023]
Abstract
Cytochrome P450 enzymes of the CYP720B subfamily play a central role in the biosynthesis of diterpene resin acids (DRAs), which are a major component of the conifer oleoresin defense system. CYP720Bs exist in families of up to a dozen different members in conifer genomes and fall into four different clades (I-IV). Only two CYP720B members, loblolly pine (Pinus taeda) PtCYP720B1 and Sitka spruce (Picea sitchensis) PsCYP720B4, have been characterized previously. Both are multisubstrate and multifunctional clade III enzymes, which catalyze consecutive three-step oxidations in the conversion of diterpene olefins to DRAs. These reactions resemble the sequential diterpene oxidations affording ent-kaurenoic acid from ent-kaurene in gibberellin biosynthesis. Here, we functionally characterized the CYP720B clade I enzymes CYP720B2 and CYP720B12 in three different conifer species, Sitka spruce, lodgepole pine (Pinus contorta), and jack pine (Pinus banksiana), and compared their activities with those of the clade III enzymes CYP720B1 and CYP720B4 of the same species. Unlike the clade III enzymes, clade I enzymes were ultimately found not to be active with diterpene olefins but converted the recently discovered, unstable diterpene synthase product 13-hydroxy-8(14)-abietene. Through alternative routes, CYP720B enzymes of both clades produce some of the same profiles of conifer oleoresin DRAs (abietic acid, neoabietic acid, levopimaric acid, and palustric acid), while clade III enzymes also function in the formation of pimaric acid, isopimaric acid, and sandaracopimaric acid. These results highlight the modularity of the specialized (i.e. secondary) diterpene metabolism, which produces conifer defense metabolites through variable combinations of different diterpene synthase and CYP720B enzymes.
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Affiliation(s)
- Katrin Geisler
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Niels Berg Jensen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Macaire M S Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Lina Madilao
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
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Keeling CI, Li M, Sandhu HK, Henderson H, Yuen MMS, Bohlmann J. Quantitative metabolome, proteome and transcriptome analysis of midgut and fat body tissues in the mountain pine beetle, Dendroctonus ponderosae Hopkins, and insights into pheromone biosynthesis. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 70:170-183. [PMID: 26792242 DOI: 10.1016/j.ibmb.2016.01.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Revised: 12/30/2015] [Accepted: 01/05/2016] [Indexed: 06/05/2023]
Abstract
Bark beetles (Coleoptera: Scolytinae) are pests of many forests around the world. The mountain pine beetle (MPB), Dendroctonus ponderosae Hopkins, is a significant pest of western North American pine forests. The MPB is able to overcome the defences of pine trees through pheromone-assisted aggregation that results in a mass attack of host trees. These pheromones, both male and female produced, are believed to be biosynthesized in the midgut and/or fat bodies of these insects. We used metabolite analysis, quantitative proteomics (iTRAQ) and transcriptomics (RNA-seq) to identify proteins and transcripts differentially expressed between sexes and between tissues when treated with juvenile hormone III. Juvenile hormone III induced frontalin biosynthesis in males and trans-verbenol biosynthesis in females, as well as affected the expression of many proteins and transcripts in sex- and tissue-specific ways. Based on these analyses, we identified candidate genes involved in the biosynthesis of frontalin, exo-brevicomin, and trans-verbenol pheromones.
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Affiliation(s)
- Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4.
| | - Maria Li
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4
| | - Harpreet K Sandhu
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4
| | - Hannah Henderson
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4
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Visser EA, Wegrzyn JL, Steenkmap ET, Myburg AA, Naidoo S. Combined de novo and genome guided assembly and annotation of the Pinus patula juvenile shoot transcriptome. BMC Genomics 2015; 16:1057. [PMID: 26652261 PMCID: PMC4676862 DOI: 10.1186/s12864-015-2277-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 12/06/2015] [Indexed: 11/25/2022] Open
Abstract
Background Pines are the most important tree species to the international forestry industry, covering 42 % of the global industrial forest plantation area. One of the most pressing threats to cultivation of some pine species is the pitch canker fungus, Fusarium circinatum, which can have devastating effects in both the field and nursery. Investigation of the Pinus-F. circinatum host-pathogen interaction is crucial for development of effective disease management strategies. As with many non-model organisms, investigation of host-pathogen interactions in pine species is hampered by limited genomic resources. This was partially alleviated through release of the 22 Gbp Pinus taeda v1.01 genome sequence (http://pinegenome.org/pinerefseq/) in 2014. Despite the fact that the fragmented state of the genome may hamper comprehensive transcriptome analysis, it is possible to leverage the inherent redundancy resulting from deep RNA sequencing with Illumina short reads to assemble transcripts in the absence of a completed reference sequence. These data can then be integrated with available genomic data to produce a comprehensive transcriptome resource. The aim of this study was to provide a foundation for gene expression analysis of disease response mechanisms in Pinus patula through transcriptome assembly. Results Eighteen de novo and two reference based assemblies were produced for P. patula shoot tissue. For this purpose three transcriptome assemblers, Trinity, Velvet/OASES and SOAPdenovo-Trans, were used to maximise diversity and completeness of assembled transcripts. Redundancy in the assembly was reduced using the EvidentialGene pipeline. The resulting 52 Mb P. patula v1.0 shoot transcriptome consists of 52 112 unigenes, 60 % of which could be functionally annotated. Conclusions The assembled transcriptome will serve as a major genomic resource for future investigation of P. patula and represents the largest gene catalogue produced to date for this species. Furthermore, this assembly can help detect gene-based genetic markers for P. patula and the comparative assembly workflow could be applied to generate similar resources for other non-model species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2277-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Erik A Visser
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, 06269, USA.
| | - Emma T Steenkmap
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa.
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Gene discovery for enzymes involved in limonene modification or utilization by the mountain pine beetle-associated pathogen Grosmannia clavigera. Appl Environ Microbiol 2015; 80:4566-76. [PMID: 24837377 DOI: 10.1128/aem.00670-14] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To successfully colonize and eventually kill pine trees, Grosmannia clavigera (Gs cryptic species), the main fungal pathogen associated with the mountain pine beetle (Dendroctonus ponderosae), has developed multiple mechanisms to overcome host tree chemical defenses, of which terpenoids are a major component. In addition to a monoterpene efflux system mediated by a recently discovered ABC transporter, Gs has genes that are highly induced by monoterpenes and that encode enzymes that modify or utilize monoterpenes [especially (+)-limonene]. We showed that pine-inhabiting Ophiostomale fungi are tolerant to monoterpenes, but only a few, including Gs, are known to utilize monoterpenes as a carbon source. Gas chromatography-mass spectrometry (GC-MS) revealed that Gs can modify (+)-limonene through various oxygenation pathways, producing carvone, p-mentha-2,8-dienol, perillyl alcohol, and isopiperitenol. It can also degrade (+)-limonene through the C-1-oxygenated pathway, producing limonene-1,2-diol as the most abundant intermediate. Transcriptome sequencing (RNA-seq) data indicated that Gs may utilize limonene 1,2-diol through beta-oxidation and then valine and tricarboxylic acid (TCA) metabolic pathways. The data also suggested that at least two gene clusters, located in genome contigs 108 and 161, were highly induced by monoterpenes and may be involved in monoterpene degradation processes. Further, gene knockouts indicated that limonene degradation required two distinct Baeyer-Villiger monooxygenases (BVMOs), an epoxide hydrolase and an enoyl coenzyme A (enoyl-CoA) hydratase. Our work provides information on enzyme-mediated limonene utilization or modification and a more comprehensive understanding of the interaction between an economically important fungal pathogen and its host's defense chemicals.
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Warren RL, Keeling CI, Yuen MMS, Raymond A, Taylor GA, Vandervalk BP, Mohamadi H, Paulino D, Chiu R, Jackman SD, Robertson G, Yang C, Boyle B, Hoffmann M, Weigel D, Nelson DR, Ritland C, Isabel N, Jaquish B, Yanchuk A, Bousquet J, Jones SJM, MacKay J, Birol I, Bohlmann J. Improved white spruce (Picea glauca) genome assemblies and annotation of large gene families of conifer terpenoid and phenolic defense metabolism. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:189-212. [PMID: 26017574 DOI: 10.1111/tpj.12886] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/15/2015] [Indexed: 05/21/2023]
Abstract
White spruce (Picea glauca), a gymnosperm tree, has been established as one of the models for conifer genomics. We describe the draft genome assemblies of two white spruce genotypes, PG29 and WS77111, innovative tools for the assembly of very large genomes, and the conifer genomics resources developed in this process. The two white spruce genotypes originate from distant geographic regions of western (PG29) and eastern (WS77111) North America, and represent elite trees in two Canadian tree-breeding programs. We present an update (V3 and V4) for a previously reported PG29 V2 draft genome assembly and introduce a second white spruce genome assembly for genotype WS77111. Assemblies of the PG29 and WS77111 genomes confirm the reconstructed white spruce genome size in the 20 Gbp range, and show broad synteny. Using the PG29 V3 assembly and additional white spruce genomics and transcriptomics resources, we performed MAKER-P annotation and meticulous expert annotation of very large gene families of conifer defense metabolism, the terpene synthases and cytochrome P450s. We also comprehensively annotated the white spruce mevalonate, methylerythritol phosphate and phenylpropanoid pathways. These analyses highlighted the large extent of gene and pseudogene duplications in a conifer genome, in particular for genes of secondary (i.e. specialized) metabolism, and the potential for gain and loss of function for defense and adaptation.
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Affiliation(s)
- René L Warren
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Macaire Man Saint Yuen
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Anthony Raymond
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Greg A Taylor
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Benjamin P Vandervalk
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Hamid Mohamadi
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Daniel Paulino
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Readman Chiu
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Shaun D Jackman
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Gordon Robertson
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Chen Yang
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
| | - Brian Boyle
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Margarete Hoffmann
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076, Tübingen, Germany
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Carol Ritland
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Nathalie Isabel
- Natural Resources Canada, Laurentian Forestry Centre, Québec, QC, G1V 4C7, Canada
| | - Barry Jaquish
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Alvin Yanchuk
- British Columbia Ministry of Forests, Lands, and Natural Resource Operations, Victoria, BC, V8W 9C2, Canada
| | - Jean Bousquet
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Steven J M Jones
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - John MacKay
- Department of Wood and Forest Sciences, Université Laval, Québec, QC, G1V 0A6, Canada
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Inanc Birol
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, V5Z 4S6, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6H 3N1, Canada
- School of Computing Science, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Joerg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Forest and Conservation Sciences, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
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Parker MT, Zhong Y, Dai X, Wang S, Zhao P. Comparative genomic and transcriptomic analysis of terpene synthases in Arabidopsis and Medicago. IET Syst Biol 2014; 8:146-53. [PMID: 25075527 DOI: 10.1049/iet-syb.2013.0032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study provides a timely comparative genomic and transcriptomic analysis of the terpene synthase (TPS) gene family in Medicago truncatula (bears glandular and non-glandular trichomes) and Arabidopsis thaliana (bears non-glandular trichomes). The authors' efforts aimed to gain insight into TPS function, phylogenetic relationships and the role of trichomes in terpene biosynthesis and function. In silico analysis identified 33 and 23 putative full-length TPS genes in Arabidopsis and Medicago, respectively. All AtTPS and MtTPS fall into the five established angiosperm TPS subfamilies, with lineage-specific expansion of Subfamily A in Arabidopsis and Subfamily G in Medicago. Large amounts of tandem duplication have occurred in both species, but only one syntenic duplication seems to have occurred in Arabidopsis, with no such duplication apparent in Medicago. Expression analysis indicates that there is much more trichome-localised TPS expression in Medicago than in Arabidopsis. However, TPS genes were expressed in non-glandular trichomes in both species. One trichome-specific gene has been identified in each Medicago and Arabidopsis along with flower-, seed-, stem- and root-specific genes. Of these, MtTPS11 is a promising candidate for trichome-specific genetic engineering, a technology that may be possible for both plants according to the findings of this manuscript. These results suggest that non-glandular trichomes may play a role in plant chemical defense and/or ecological communication instead of only in physical defence. Finally, the general lack of correlation between expression patterns and phylogenetic relationships in both species suggests that phylogenetic analysis alone is insufficient to predict gene function even for phylogenetically close paralogs.
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Affiliation(s)
- Michael T Parker
- Department of Biology, Millersville University of Pennsylvania, Millersville, PA 17551, USA
| | - Yuan Zhong
- Department of Biology, Millersville University of Pennsylvania, Millersville, PA 17551, USA.
| | - Xinbin Dai
- Plant Bioinformatics and Genomics Laboratory, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
| | - Shiliang Wang
- Department of Bioinformatics, J. Craig Venter Institute, 9704 Medical Center Dr., Rockville, MD 20850, USA
| | - Patrick Zhao
- Plant Bioinformatics and Genomics Laboratory, The Samuel Roberts Noble Foundation, Ardmore, OK 73401, USA
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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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Pitt C, Robert JA, Bonnett TR, Keeling CI, Bohlmann J, Huber DPW. Proteomics indicators of the rapidly shifting physiology from whole mountain pine beetle, Dendroctonus ponderosae (Coleoptera: Curculionidae), adults during early host colonization. PLoS One 2014; 9:e110673. [PMID: 25360753 PMCID: PMC4215907 DOI: 10.1371/journal.pone.0110673] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 09/16/2014] [Indexed: 01/08/2023] Open
Abstract
We developed proteome profiles for host colonizing mountain pine beetle adults, Dendroctonus ponderosae Hopkins (Coleoptera: Curculionidae). Adult insects were fed in pairs on fresh host lodgepole pine, Pinus contorta Dougl. ex Loud, phloem tissue. The proteomes of fed individuals were monitored using iTRAQ and compared to those of starved beetles, revealing 757 and 739 expressed proteins in females and males, respectively, for which quantitative information was obtained. Overall functional category distributions were similar for males and females, with the majority of proteins falling under carbohydrate metabolism (glycolysis, gluconeogenesis, citric acid cycle), structure (cuticle, muscle, cytoskeleton), and protein and amino acid metabolism. Females had 23 proteins with levels that changed significantly with feeding (p<0.05, FDR<0.20), including chaperones and enzymes required for vitellogenesis. In males, levels of 29 proteins changed significantly with feeding (p<0.05, FDR<0.20), including chaperones as well as motor proteins. Only two proteins, both chaperones, exhibited a significant change in both females and males with feeding. Proteins with differential accumulation patterns in females exhibited higher fold changes with feeding than did those in males. This difference may be due to major and rapid physiological changes occurring in females upon finding a host tree during the physiological shift from dispersal to reproduction. The significant accumulation of chaperone proteins, a cytochrome P450, and a glutathione S-transferase, indicate secondary metabolite-induced stress physiology related to chemical detoxification during early host colonization. The females' activation of vitellogenin only after encountering a host indicates deliberate partitioning of resources and a balancing of the needs of dispersal and reproduction.
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Affiliation(s)
- Caitlin Pitt
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, Canada
- * E-mail: (DH); (CP)
| | - Jeanne A. Robert
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, Canada
| | - Tiffany R. Bonnett
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, Canada
| | | | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, Canada
| | - Dezene P. W. Huber
- Ecosystem Science and Management Program, University of Northern British Columbia, Prince George, BC, Canada
- * E-mail: (DH); (CP)
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Comparative analysis and validation of the malachite green assay for the high throughput biochemical characterization of terpene synthases. MethodsX 2014; 1:187-96. [PMID: 26150952 PMCID: PMC4472957 DOI: 10.1016/j.mex.2014.08.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 08/15/2014] [Indexed: 11/21/2022] Open
Abstract
Terpenes are the largest group of natural products with important and diverse biological roles, while of tremendous economic value as fragrances, flavours and pharmaceutical agents. Class-I terpene synthases (TPSs), the dominant type of TPS enzymes, catalyze the conversion of prenyl diphosphates to often structurally diverse bioactive terpene hydrocarbons, and inorganic pyrophosphate (PPi). To measure their kinetic properties, current bio-analytical methods typically rely on the direct detection of hydrocarbon products by radioactivity measurements or gas chromatography-mass spectrometry (GC-MS). In this study we employed an established, rapid colorimetric assay, the pyrophosphate/malachite green assay (MG), as an alternative means for the biochemical characterization of class I TPSs activity.•We describe the adaptation of the MG assay for turnover and catalytic efficiency measurements of TPSs.•We validate the method by direct comparison with established assays. The agreement of k cat/K M among methods makes this adaptation optimal for rapid evaluation of TPSs.•We demonstrate the application of the MG assay for the high-throughput screening of TPS gene libraries.
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Massoumi Alamouti S, Haridas S, Feau N, Robertson G, Bohlmann J, Breuil C. Comparative Genomics of the Pine Pathogens and Beetle Symbionts in the Genus Grosmannia. Mol Biol Evol 2014; 31:1454-74. [DOI: 10.1093/molbev/msu102] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Keeling CI, Henderson H, Li M, Dullat HK, Ohnishi T, Bohlmann J. CYP345E2, an antenna-specific cytochrome P450 from the mountain pine beetle, Dendroctonus ponderosae Hopkins, catalyses the oxidation of pine host monoterpene volatiles. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 43:1142-1151. [PMID: 24139909 DOI: 10.1016/j.ibmb.2013.10.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Revised: 09/27/2013] [Accepted: 10/02/2013] [Indexed: 06/02/2023]
Abstract
The mountain pine beetle (MPB, Dendroctonus ponderosae Hopkins) is a significant pest of western North American pine forests. This beetle responds to pheromones and host volatiles in order to mass attack and thus overcome the terpenoid chemical defences of its host. The ability of MPB antennae to rapidly process odorants is necessary to avoid odorant receptor saturation and thus the enzymes responsible for odorant clearance are an important aspect of host colonization. An antenna-specific cytochrome P450, DponCYP345E2, is the most highly expressed transcript in adult MPB antenna. In in vitro assays with recombinant enzyme, DponCYP345E2 used several pine host monoterpenes as substrates, including (+)-(3)-carene, (+)-β-pinene, (-)-β-pinene, (+)-limonene, (-)-limonene, (-)-camphene, (+)-α-pinene, (-)-α-pinene, and terpinolene. The substrates were epoxidized or hydroxylated, depending upon the substrate. To complement DponCYP345E2, we also functionally characterized the NADPH-dependent cytochrome P450 reductase and the cytochrome b5 from MPB. DponCYP345E2 is the first cytochrome P450 to be functionally characterized in insect olfaction and in MPB.
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Affiliation(s)
- Christopher I Keeling
- Michael Smith Laboratories, University of British Columbia, 301-2185 East Mall, Vancouver, BC, Canada V6T 1A4.
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