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Mishra S, Zhang X, Yang X. Plant communication with rhizosphere microbes can be revealed by understanding microbial functional gene composition. Microbiol Res 2024; 284:127726. [PMID: 38643524 DOI: 10.1016/j.micres.2024.127726] [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: 12/30/2023] [Revised: 03/26/2024] [Accepted: 04/12/2024] [Indexed: 04/23/2024]
Abstract
Understanding rhizosphere microbial ecology is necessary to reveal the interplay between plants and associated microbial communities. The significance of rhizosphere-microbial interactions in plant growth promotion, mediated by several key processes such as auxin synthesis, enhanced nutrient uptake, stress alleviation, disease resistance, etc., is unquestionable and well reported in numerous literature. Moreover, rhizosphere research has witnessed tremendous progress due to the integration of the metagenomics approach and further shift in our viewpoint from taxonomic to functional diversity over the past decades. The microbial functional genes corresponding to the beneficial functions provide a solid foundation for the successful establishment of positive plant-microbe interactions. The microbial functional gene composition in the rhizosphere can be regulated by several factors, e.g., the nutritional requirements of plants, soil chemistry, soil nutrient status, pathogen attack, abiotic stresses, etc. Knowing the pattern of functional gene composition in the rhizosphere can shed light on the dynamics of rhizosphere microbial ecology and the strength of cooperation between plants and associated microbes. This knowledge is crucial to realizing how microbial functions respond to unprecedented challenges which are obvious in the Anthropocene. Unraveling how microbes-mediated beneficial functions will change under the influence of several challenges, requires knowledge of the pattern and composition of functional genes corresponding to beneficial functions such as biogeochemical functions (nutrient cycle), plant growth promotion, stress mitigation, etc. Here, we focus on the molecular traits of plant growth-promoting functions delivered by a set of microbial functional genes that can be useful to the emerging field of rhizosphere functional ecology.
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Affiliation(s)
- Sandhya Mishra
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
| | - Xianxian Zhang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaodong Yang
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, Yunnan 666303, China.
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2
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Feitosa-Junior OR, Lubbe A, Kosina SM, Martins-Junior J, Barbosa D, Baccari C, Zaini PA, Bowen BP, Northen TR, Lindow SE, da Silva AM. The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones. Metabolites 2024; 14:82. [PMID: 38392974 PMCID: PMC10890622 DOI: 10.3390/metabo14020082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/25/2024] Open
Abstract
Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall-degrading enzymes, adhesion proteins, and quorum-sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with the Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. Liquid chromatography-mass spectrometry (LC-MS) and the Method for Metabolite Annotation and Gene Integration (MAGI) were used to detect and map metabolites to genomes, revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of a P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-aminoisobutyric acid and gibberellic acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.
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Affiliation(s)
- Oseias R Feitosa-Junior
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Andrea Lubbe
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joaquim Martins-Junior
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
| | - Deibs Barbosa
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
| | - Clelia Baccari
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Benjamin P Bowen
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R Northen
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven E Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
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Heiden N, Broders KA, Hutin M, Castro MO, Roman-Reyna V, Toth H, Jacobs JM. Bacterial Leaf Streak Diseases of Plants: Symptom Convergence in Monocot Plants by Distant Pathogenic Xanthomonas Species. PHYTOPATHOLOGY 2023; 113:2048-2055. [PMID: 37996392 DOI: 10.1094/phyto-05-23-0155-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Bacterial leaf streak (BLS) is a disease of monocot plants caused by Xanthomonas translucens on small grains, X. vasicola on maize and sorghum, and X. oryzae on rice. These three pathogens cause remarkably similar symptomology in their host plants. Despite causing similar symptoms, BLS pathogens are dispersed throughout the larger Xanthomonas phylogeny. Each aforementioned species includes strain groups that do not cause BLS and instead cause vascular disease. In this commentary, we hypothesize that strains of X. translucens, X. vasicola, and X. oryzae convergently evolved to cause BLS due to shared evolutionary pressures. We examined the diversity of secreted effectors, which may be important virulence factors for BLS pathogens and their evolution. We discuss evidence that differences in gene regulation and abilities to manipulate plant hormones may also separate BLS pathogens from other Xanthomonas species or pathovars. BLS is becoming an increasing issue across the three pathosystems. Overall, we hope that a better understanding of conserved mechanisms used by BLS pathogens will enable researchers to translate findings across production systems and guide approaches to control this (re)emerging threat.
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Affiliation(s)
- Nathaniel Heiden
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Kirk A Broders
- U.S. Department of Agriculture-Agricultural Research Service, National Center for Agricultural Utilization Research, Mycotoxin Prevention and Applied Microbiology Research Unit, Peoria, IL 61604, U.S.A
| | - Mathilde Hutin
- Plant Health Institute of Montpellier, University of Montpellier, IRD, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Mary Ortiz Castro
- Horticulture and Extension Programs, Colorado State University, Castle Rock, CO 80106, U.S.A
| | - Verónica Roman-Reyna
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
- Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA 16802, U.S.A
| | - Hannah Toth
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
| | - Jonathan M Jacobs
- Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, U.S.A
- Infectious Diseases Institute, The Ohio State University, Columbus, OH 43210, U.S.A
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Wang Y, Li T, Sun Z, Huang X, Yu N, Tai H, Yang Q. Comparative transcriptome meta-analysis reveals a set of genes involved in the responses to multiple pathogens in maize. FRONTIERS IN PLANT SCIENCE 2022; 13:971371. [PMID: 36186003 PMCID: PMC9521429 DOI: 10.3389/fpls.2022.971371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Maize production is constantly threatened by the presence of different fungal pathogens worldwide. Genetic resistance is the most favorable approach to reducing yield losses resulted from fungal diseases. The molecular mechanism underlying disease resistance in maize remains largely unknown. The objective of this study was to identify key genes/pathways that are consistently associated with multiple fungal pathogen infections in maize. Here, we conducted a meta-analysis of gene expression profiles from seven publicly available RNA-seq datasets of different fungal pathogen infections in maize. We identified 267 common differentially expressed genes (co-DEGs) in the four maize leaf infection experiments and 115 co-DEGs in all the seven experiments. Functional enrichment analysis showed that the co-DEGs were mainly involved in the biosynthesis of diterpenoid and phenylpropanoid. Further investigation revealed a set of genes associated with terpenoid phytoalexin and lignin biosynthesis, as well as potential pattern recognition receptors and nutrient transporter genes, which were consistently up-regulated after inoculation with different pathogens. In addition, we constructed a weighted gene co-expression network and identified several hub genes encoding transcription factors and protein kinases. Our results provide valuable insights into the pathways and genes influenced by different fungal pathogens, which might facilitate mining multiple disease resistance genes in maize.
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Affiliation(s)
- Yapeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Zedan Sun
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Xiaojian Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Naibing Yu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Huanhuan Tai
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Qin Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, China
- Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, Northwest A&F University, Yangling, China
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Nett RS, Bender KS, Peters RJ. Production of the plant hormone gibberellin by rhizobia increases host legume nodule size. THE ISME JOURNAL 2022; 16:1809-1817. [PMID: 35414717 PMCID: PMC9213532 DOI: 10.1038/s41396-022-01236-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 12/11/2022]
Abstract
Plant-associated microbes have evolved the ability to independently produce gibberellin (GA) phytohormones as a mechanism to influence their host. Indeed, GA was first discovered as a metabolite from the fungal rice pathogen Gibberella fujikuroi, which uses it as a virulence factor. Though some bacterial plant pathogens similarly use GA to promote infection, symbiotic nitrogen-fixing bacteria (rhizobia), which inhabit the root nodules of legumes, also can produce GA, suggesting a role in symbiosis. The bacterial GA biosynthetic operon has been identified, but in rhizobia this typically no longer encodes the final metabolic gene (cyp115), so that these symbionts can only produce the penultimate intermediate GA9. Here, we demonstrate that soybean (Glycine max) expresses functional GA 3-oxidases (GA3ox) within its nodules, which have the capability to convert GA9 produced by the enclosed rhizobial symbiont Bradyrhizobium diazoefficiens to bioactive GA4. This rhizobia-derived GA is demonstrated to cause an increase in nodule size and decrease in the number of nodules. The increase in individual nodule size correlates to greater numbers of bacterial progeny within a nodule, thereby providing a selective advantage to rhizobia that produce GA during the rhizobia-legume symbiosis. The expression of GA3ox in nodules and resultant nodulation effects of the GA product suggests that soybean has co-opted control of bioactive GA production, and thus nodule size, for its own benefit. Thus, our results suggest rhizobial GA biosynthesis has coevolved with host plant metabolism for cooperative production of a phytohormone that influences nodulation in a mutually beneficial manner.
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Affiliation(s)
- Ryan S Nett
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Kelly S Bender
- Department of Microbiology, Southern Illinois University, Carbondale, IL, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, 50011, USA.
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Ong CE, Ahmad R, Goh YK, Azizan KA, Baharum SN, Goh KJ. Growth modulation and metabolic responses of Ganoderma boninense to salicylic acid stress. PLoS One 2021; 16:e0262029. [PMID: 34972183 PMCID: PMC8719765 DOI: 10.1371/journal.pone.0262029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 12/15/2021] [Indexed: 12/03/2022] Open
Abstract
Various phenolic compounds have been screened against Ganoderma boninense, the fungal pathogen causing basal stem rot in oil palms. In this study, we focused on the effects of salicylic acid (SA) on the growth of three G. boninense isolates with different levels of aggressiveness. In addition, study on untargeted metabolite profiling was conducted to investigate the metabolomic responses of G. boninense towards salicylic acid. The inhibitory effects of salicylic acid were both concentration- (P < 0.001) and isolate-dependent (P < 0.001). Also, growth-promoting effect was observed in one of the isolates at low concentrations of salicylic acid where it could have been utilized by G. boninense as a source of carbon and energy. Besides, adaptation towards salicylic acid treatment was evident in this study for all isolates, particularly at high concentrations. In other words, inhibitory effect of salicylic acid treatment on the fungal growth declined over time. In terms of metabolomics response to salicylic acid treatment, G. boninense produced several metabolites such as coumarin and azatyrosine, which suggests that salicylic acid modulates the developmental switch in G. boninense towards the defense mode for its survival. Furthermore, the liquid chromatography time-of-flight mass spectrometry (LC-TOF-MS) analysis showed that the growth of G. boninense on potato dextrose agar involved at least four metabolic pathways: amino acid metabolism, lipid pathway, tryptophan pathway and phenylalanine pathway. Overall, there were 17 metabolites that contributed to treatment separation, each with P<0.005. The release of several antimicrobial metabolites such as eudistomin I may enhance G. boninense's competitiveness against other microorganisms during colonisation. Our findings demonstrated the metabolic versatility of G. boninense towards changes in carbon sources and stress factors. G. boninense was shown to be capable of responding to salicylic acid treatment by switching its developmental stage.
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Affiliation(s)
- Cu Ean Ong
- Advanced Agriecological Research Sdn. Bhd., Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Rafidah Ahmad
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - You Keng Goh
- Advanced Agriecological Research Sdn. Bhd., Kota Damansara, Petaling Jaya, Selangor, Malaysia
| | - Kamalrul Azlan Azizan
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Syarul Nataqain Baharum
- Metabolomics Research Laboratory, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia (UKM), Bangi, Selangor, Malaysia
| | - Kah Joo Goh
- Advanced Agriecological Research Sdn. Bhd., Kota Damansara, Petaling Jaya, Selangor, Malaysia
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Yu Y, Tan H, Liu T, Liu L, Tang J, Peng W. Dual RNA-Seq Analysis of the Interaction Between Edible Fungus Morchella sextelata and Its Pathogenic Fungus Paecilomyces penicillatus Uncovers the Candidate Defense and Pathogenic Factors. Front Microbiol 2021; 12:760444. [PMID: 34925269 PMCID: PMC8675245 DOI: 10.3389/fmicb.2021.760444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Morels (Morchella spp.) are economically important mushrooms cultivated in many countries. However, their production and quality are hindered by white mold disease because of Paecilomyces penicillatus infection. In this study, we aimed to understand the genetic mechanisms of interactions between P. penicillatus and Morchella. M. sextelata, the most prevalent species of Morchella in China, was inoculated with P. penicillatus; then, the expression profiles of both fungi were determined simultaneously at 3 and 6 days post-inoculation (dpi) using a dual RNA-Seq approach. A total of 460 and 313 differentially expressed genes (DEGs) were identified in P. penicillatus and M. sextelata, respectively. The CAZymes of β-glucanases and mannanases, as well as subtilase family, were upregulated in P. penicillatus, which might be involved in the degradation of M. sextelata cell walls. Chitin recognition protein, caffeine-induced death protein, and putative apoptosis-inducing protein were upregulated, while cyclin was downregulated in infected M. sextelata. This indicates that P. penicillatus could trigger programmed cell death in M. sextelata after infection. Laccase-2, tyrosinases, and cytochrome P450s were also upregulated in M. sextelata. The increased expression levels of these genes suggest that M. sextelata could detoxify the P. penicillatus toxins and also form a melanin barrier against P. penicillatus invasion. The potential pathogenic mechanisms of P. penicillatus on M. sextelata and the defense mechanisms of M. sextelata against P. penicillatus were well described.
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Affiliation(s)
- Yang Yu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China.,National Observing and Experimental Station of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Hao Tan
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China.,National Observing and Experimental Station of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Chengdu, China.,School of Bioengineering, Jiangnan University, Wuxi, China
| | - Tianhai Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China.,National Observing and Experimental Station of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Lixu Liu
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China.,National Observing and Experimental Station of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Jie Tang
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China.,National Observing and Experimental Station of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Weihong Peng
- National-Local Joint Engineering Laboratory of Breeding and Cultivation of Edible and Medicinal Fungi, Institute of Agricultural Resources and Environment, Sichuan Academy of Agricultural Sciences, Chengdu, China.,National Observing and Experimental Station of Agricultural Microbiology, Ministry of Agriculture and Rural Affairs, Chengdu, China
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Gorshkov V, Tsers I. Plant susceptible responses: the underestimated side of plant-pathogen interactions. Biol Rev Camb Philos Soc 2021; 97:45-66. [PMID: 34435443 PMCID: PMC9291929 DOI: 10.1111/brv.12789] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/18/2022]
Abstract
Plant susceptibility to pathogens is usually considered from the perspective of the loss of resistance. However, susceptibility cannot be equated with plant passivity since active host cooperation may be required for the pathogen to propagate and cause disease. This cooperation consists of the induction of reactions called susceptible responses that transform a plant from an autonomous biological unit into a component of a pathosystem. Induced susceptibility is scarcely discussed in the literature (at least compared to induced resistance) although this phenomenon has a fundamental impact on plant-pathogen interactions and disease progression. This review aims to summarize current knowledge on plant susceptible responses and their regulation. We highlight two main categories of susceptible responses according to their consequences and indicate the relevance of susceptible response-related studies to agricultural practice. We hope that this review will generate interest in this underestimated aspect of plant-pathogen interactions.
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Affiliation(s)
- Vladimir Gorshkov
- Kazan Institute of Biochemistry and Biophysics, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, 420111, Russia.,Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, 420111, Russia
| | - Ivan Tsers
- Laboratory of Plant Infectious Diseases, Federal Research Center Kazan Scientific Center of Russian Academy of Sciences, Kazan, 420111, Russia
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Eichmann R, Richards L, Schäfer P. Hormones as go-betweens in plant microbiome assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:518-541. [PMID: 33332645 PMCID: PMC8629125 DOI: 10.1111/tpj.15135] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 05/04/2023]
Abstract
The interaction of plants with complex microbial communities is the result of co-evolution over millions of years and contributed to plant transition and adaptation to land. The ability of plants to be an essential part of complex and highly dynamic ecosystems is dependent on their interaction with diverse microbial communities. Plant microbiota can support, and even enable, the diverse functions of plants and are crucial in sustaining plant fitness under often rapidly changing environments. The composition and diversity of microbiota differs between plant and soil compartments. It indicates that microbial communities in these compartments are not static but are adjusted by the environment as well as inter-microbial and plant-microbe communication. Hormones take a crucial role in contributing to the assembly of plant microbiomes, and plants and microbes often employ the same hormones with completely different intentions. Here, the function of hormones as go-betweens between plants and microbes to influence the shape of plant microbial communities is discussed. The versatility of plant and microbe-derived hormones essentially contributes to the creation of habitats that are the origin of diversity and, thus, multifunctionality of plants, their microbiota and ultimately ecosystems.
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Affiliation(s)
- Ruth Eichmann
- Institute of Molecular BotanyUlm UniversityUlm89069Germany
| | - Luke Richards
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
| | - Patrick Schäfer
- Institute of Molecular BotanyUlm UniversityUlm89069Germany
- School of Life SciencesUniversity of WarwickCoventryCV4 7ALUK
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Hedden P. The Current Status of Research on Gibberellin Biosynthesis. PLANT & CELL PHYSIOLOGY 2020; 61:1832-1849. [PMID: 32652020 PMCID: PMC7758035 DOI: 10.1093/pcp/pcaa092] [Citation(s) in RCA: 123] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/21/2020] [Indexed: 05/23/2023]
Abstract
Gibberellins are produced by all vascular plants and several fungal and bacterial species that associate with plants as pathogens or symbionts. In the 60 years since the first experiments on the biosynthesis of gibberellic acid in the fungus Fusarium fujikuroi, research on gibberellin biosynthesis has advanced to provide detailed information on the pathways, biosynthetic enzymes and their genes in all three kingdoms, in which the production of the hormones evolved independently. Gibberellins function as hormones in plants, affecting growth and differentiation in organs in which their concentration is very tightly regulated. Current research in plants is focused particularly on the regulation of gibberellin biosynthesis and inactivation by developmental and environmental cues, and there is now considerable information on the molecular mechanisms involved in these processes. There have also been recent advances in understanding gibberellin transport and distribution and their relevance to plant development. This review describes our current understanding of gibberellin metabolism and its regulation, highlighting the more recent advances in this field.
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Affiliation(s)
- Peter Hedden
- Laboratory of Growth Regulators, Palack� University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, 78371 Olomouc, Czech Republic
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
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Abstract
Gibberellin (GA) phytohormones are ubiquitous regulators of growth and developmental processes in vascular plants. The convergent evolution of GA production by plant-associated bacteria, including both symbiotic nitrogen-fixing rhizobia and phytopathogens, suggests that manipulation of GA signaling is a powerful mechanism for microbes to gain an advantage in these interactions. Although orthologous operons encode GA biosynthetic enzymes in both rhizobia and phytopathogens, notable genetic heterogeneity and scattered operon distribution in these lineages, including loss of the gene for the final biosynthetic step in most rhizobia, suggest varied functions for GA in these distinct plant-microbe interactions. Therefore, deciphering GA operon evolutionary history should provide crucial evidence toward understanding the distinct biological roles for bacterial GA production. To further establish the genetic composition of the GA operon, two operon-associated genes that exhibit limited distribution among rhizobia were biochemically characterized, verifying their roles in GA biosynthesis. This enabled employment of a maximum parsimony ancestral gene block reconstruction algorithm to characterize loss, gain, and horizontal gene transfer (HGT) of GA operon genes within alphaproteobacterial rhizobia, which exhibit the most heterogeneity among the bacteria containing this biosynthetic gene cluster. Collectively, this evolutionary analysis reveals a complex history for HGT of the entire GA operon, as well as the individual genes therein, and ultimately provides a basis for linking genetic content to bacterial GA functions in diverse plant-microbe interactions, including insight into the subtleties of the coevolving molecular interactions between rhizobia and their leguminous host plants.IMPORTANCE While production of phytohormones by plant-associated microbes has long been appreciated, identification of the gibberellin (GA) biosynthetic operon in plant-associated bacteria has revealed surprising genetic heterogeneity. Notably, this heterogeneity seems to be associated with the lifestyle of the microbe; while the GA operon in phytopathogenic bacteria does not seem to vary to any significant degree, thus enabling production of bioactive GA, symbiotic rhizobia exhibit a number of GA operon gene loss and gain events. This suggests that a unique set of selective pressures are exerted on this biosynthetic gene cluster in rhizobia. Through analysis of the evolutionary history of the GA operon in alphaproteobacterial rhizobia, which display substantial diversity in their GA operon structure and gene content, we provide insight into the effect of lifestyle and host interactions on the production of this phytohormone by plant-associated bacteria.
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12
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Ding Y, Murphy KM, Poretsky E, Mafu S, Yang B, Char SN, Christensen SA, Saldivar E, Wu M, Wang Q, Ji L, Schmitz RJ, Kremling KA, Buckler ES, Shen Z, Briggs SP, Bohlmann J, Sher A, Castro-Falcon G, Hughes CC, Huffaker A, Zerbe P, Schmelz EA. Multiple genes recruited from hormone pathways partition maize diterpenoid defences. NATURE PLANTS 2019; 5:1043-1056. [PMID: 31527844 DOI: 10.1038/s41477-019-0509-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/26/2019] [Indexed: 06/10/2023]
Abstract
Duplication and divergence of primary pathway genes underlie the evolution of plant specialized metabolism; however, mechanisms partitioning parallel hormone and defence pathways are often speculative. For example, the primary pathway intermediate ent-kaurene is essential for gibberellin biosynthesis and is also a proposed precursor for maize antibiotics. By integrating transcriptional coregulation patterns, genome-wide association studies, combinatorial enzyme assays, proteomics and targeted mutant analyses, we show that maize kauralexin biosynthesis proceeds via the positional isomer ent-isokaurene formed by a diterpene synthase pair recruited from gibberellin metabolism. The oxygenation and subsequent desaturation of ent-isokaurene by three promiscuous cytochrome P450s and a new steroid 5α reductase indirectly yields predominant ent-kaurene-associated antibiotics required for Fusarium stalk rot resistance. The divergence and differential expression of pathway branches derived from multiple duplicated hormone-metabolic genes minimizes dysregulation of primary metabolism via the circuitous biosynthesis of ent-kaurene-related antibiotics without the production of growth hormone precursors during defence.
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Affiliation(s)
- Yezhang Ding
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Katherine M Murphy
- Department of Plant Biology, University of California Davis, Davis, CA, USA
| | - Elly Poretsky
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Sibongile Mafu
- Department of Plant Biology, University of California Davis, Davis, CA, USA
| | - Bing Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Si Nian Char
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA
| | - Shawn A Christensen
- Chemistry Research Unit, Center for Medical, Agricultural, and Veterinary Entomology, US Department of Agriculture-Agricultural Research Service, Gainesville, FL, USA
| | - Evan Saldivar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Mengxi Wu
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Qiang Wang
- Institute of Ecological Agriculture, Sichuan Agricultural University, Chengdu, China
| | - Lexiang Ji
- Institute of Bioinformatics, University of Georgia, Athens, GA, USA
| | | | - Karl A Kremling
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
| | - Edward S Buckler
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY, USA
- Robert W. Holley Center for Agriculture and Health, US Department of Agriculture-Agricultural Research Service, Ithaca, NY, USA
| | - Zhouxin Shen
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Steven P Briggs
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Jörg Bohlmann
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrew Sher
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Gabriel Castro-Falcon
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Chambers C Hughes
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
| | - Alisa Huffaker
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Philipp Zerbe
- Department of Plant Biology, University of California Davis, Davis, CA, USA
| | - Eric A Schmelz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
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13
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Nagel R, Bieber JE, Schmidt-Dannert MG, Nett RS, Peters RJ. A Third Class: Functional Gibberellin Biosynthetic Operon in Beta-Proteobacteria. Front Microbiol 2018; 9:2916. [PMID: 30546353 PMCID: PMC6278637 DOI: 10.3389/fmicb.2018.02916] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 11/13/2018] [Indexed: 11/13/2022] Open
Abstract
The ability of plant-associated microbes to produce gibberellin A (GA) phytohormones was first described for the fungal rice pathogen Gibberella fujikuroi in the 1930s. Recently the capacity to produce GAs was shown for several bacteria, including symbiotic alpha-proteobacteria (α-rhizobia) and gamma-proteobacteria phytopathogens. All necessary enzymes for GA production are encoded by a conserved operon, which appears to have undergone horizontal transfer between and within these two phylogenetic classes of bacteria. Here the operon was shown to be present and functional in a third class, the beta-proteobacteria, where it is found in several symbionts (β-rhizobia). Conservation of function was examined by biochemical characterization of the enzymes encoded by the operon from Paraburkholderia mimosarum LMG 23256T. Despite the in-frame gene fusion between the short-chain alcohol dehydrogenase/reductase and ferredoxin, the encoded enzymes exhibited the expected activity. Intriguingly, together these can only produce GA9, the immediate precursor to the bioactive GA4, as the cytochrome P450 (CYP115) that catalyzes the final hydroxylation reaction is missing, similar to most α-rhizobia. However, phylogenetic analysis indicates that the operon from β-rhizobia is more closely related to examples from gamma-proteobacteria, which almost invariably have CYP115 and, hence, can produce bioactive GA4. This indicates not only that β-rhizobia acquired the operon by horizontal gene transfer from gamma-proteobacteria, rather than α-rhizobia, but also that they independently lost CYP115 in parallel to the α-rhizobia, further hinting at the possibility of detrimental effects for the production of bioactive GA4 by these symbionts.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - John E Bieber
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States.,Science Department, Newton Senior High School, Newton, IA, United States
| | - Mark G Schmidt-Dannert
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Ryan S Nett
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA, United States
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14
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Salazar-Cerezo S, Martínez-Montiel N, García-Sánchez J, Pérez-Y-Terrón R, Martínez-Contreras RD. Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria. Microbiol Res 2018; 208:85-98. [PMID: 29551215 DOI: 10.1016/j.micres.2018.01.010] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/24/2018] [Accepted: 01/27/2018] [Indexed: 11/26/2022]
Abstract
Gibberellins (GAs) are natural complex biomolecules initially identified as secondary metabolites in the fungus Gibberella fujikuroi with strong implications in plant physiology. GAs have been identified in different fungal and bacterial species, in some cases related to virulence, but the full understanding of the role of these metabolites in the different organisms would need additional investigation. In this review, we summarize the current evidence regarding a common pathway for GA synthesis in fungi, bacteria and plant from the genes depicted as part of the GA production cluster to the enzymes responsible for the catalytic transformations and the biosynthetical routes involved. Moreover, we present the relationship between these observations and the biotechnological applications of GAs in plants, which has shown an enormous commercial impact.
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Affiliation(s)
- Sonia Salazar-Cerezo
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif 103J, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
| | - Nancy Martínez-Montiel
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif 103J, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
| | - Jenny García-Sánchez
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif 103J, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico
| | | | - Rebeca D Martínez-Contreras
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Edif 103J, Ciudad Universitaria, Col. San Manuel, CP 72570, Puebla, Mexico.
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15
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Kunkel BN, Harper CP. The roles of auxin during interactions between bacterial plant pathogens and their hosts. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:245-254. [PMID: 29272462 DOI: 10.1093/jxb/erx447] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Plant pathogens have evolved several strategies to manipulate the biology of their hosts to facilitate colonization, growth to high levels in plant tissue, and production of disease. One of the less well known of these strategies is the synthesis of plant hormones and hormone analogs, and there is growing evidence that modulation of host hormone signaling is important during pathogenesis. Several plant pathogens produce the auxin indole-3-acetic acid (IAA) and/or virulence factors that modulate host auxin signaling. Auxin is well known for being involved in many aspects of plant growth and development, but recent findings have revealed that elevated IAA levels or enhanced auxin signaling can also promote disease development in some plant-pathogen interactions. In addition to stimulating plant cell growth during infection by gall-forming bacteria, auxin and auxin signaling can antagonize plant defense responses. Auxin can also act as a microbial signaling molecule to impact the biology of some pathogens directly. In this review, we summarize recent progress towards elucidating the roles that auxin production, modification of host auxin signaling, and direct effects of auxin on pathogens play during pathogenesis, with emphasis on the impacts of auxin on interactions with bacterial pathogens.
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Affiliation(s)
- Barbara N Kunkel
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
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16
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Nagel R, Turrini PCG, Nett RS, Leach JE, Verdier V, Van Sluys MA, Peters RJ. An operon for production of bioactive gibberellin A 4 phytohormone with wide distribution in the bacterial rice leaf streak pathogen Xanthomonas oryzae pv. oryzicola. THE NEW PHYTOLOGIST 2017; 214:1260-1266. [PMID: 28134995 PMCID: PMC5388578 DOI: 10.1111/nph.14441] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/10/2016] [Indexed: 05/19/2023]
Abstract
Phytopathogens have developed elaborate mechanisms to attenuate the defense response of their host plants, including convergent evolution of complex pathways for production of the GA phytohormones, which were actually first isolated from the rice fungal pathogen Gibberella fujikuroi. The rice bacterial pathogen Xanthomonas oryzae pv. oryzicola (Xoc) has been demonstrated to contain a biosynthetic operon with cyclases capable of producing the universal GA precursor ent-kaurene. Genetic (knock-out) studies indicate that the derived diterpenoid serves as a virulence factor for this rice leaf streak pathogen, serving to reduce the jasmonic acid-mediated defense response. Here the functions of the remaining genes in the Xoc operon are elucidated and the distribution of the operon in X. oryzae is investigated in over 100 isolates. The Xoc operon leads to production of the bioactive GA4 , an additional step beyond production of the penultimate precursor GA9 mediated by the homologous operons recently characterized from rhizobia. Moreover, this GA biosynthetic operon was found to be widespread in Xoc (> 90%), but absent in the other major X. oryzae pathovar. These results indicate selective pressure for production of GA4 in the distinct lifestyle of Xoc, and the importance of GA to both fungal and bacterial pathogens of rice.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Paula C. G. Turrini
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Ryan S. Nett
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jan E. Leach
- Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523, USA
| | - Valérie Verdier
- IRD – Cirad – Univ. Montpellier, UMR Interactions Plantes Microorganismes Environnement (IPME), 34399 Montpellier, France
| | - Marie-Anne Van Sluys
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, São Paulo, São Paulo, Brasil
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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17
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Pelot KA, Hagelthorn LM, Addison JB, Zerbe P. Biosynthesis of the oxygenated diterpene nezukol in the medicinal plant Isodon rubescens is catalyzed by a pair of diterpene synthases. PLoS One 2017; 12:e0176507. [PMID: 28445526 PMCID: PMC5405970 DOI: 10.1371/journal.pone.0176507] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/11/2017] [Indexed: 01/09/2023] Open
Abstract
Plants produce an immense diversity of natural products (i.e. secondary or specialized metabolites) that offer a rich source of known and potentially new pharmaceuticals and other desirable bioproducts. The Traditional Chinese Medicinal plant Isodon rubescens (Lamiaceae) contains an array of bioactive labdane-related diterpenoid natural products. Of these, the ent-kauranoid oridonin is the most prominent specialized metabolite that has been extensively studied for its potent antimicrobial and anticancer efficacy. Mining of a previously established transcriptome of I. rubescens leaf tissue identified seven diterpene synthase (diTPSs) candidates. Here we report the functional characterization of four I. rubescens diTPSs. IrTPS5 and IrTPS3 were identified as an ent-copalyl diphosphate (CPP) synthase and a (+)-CPP synthase, respectively. Distinct transcript abundance of IrTPS5 and the predicted ent-CPP synthase IrTPS1 suggested a role of IrTPS5 in specialized ent-kaurene metabolism possibly en route to oridonin. Nicotiana benthamiana co-expression assays demonstrated that IrTPS4 functions sequentially with IrTPS3 to form miltiradiene. In addition, IrTPS2 converted the IrTPS3 product (+)-CPP into the hydroxylated tricyclic diterpene nezukol not previously identified in I. rubescens. Metabolite profiling verified the presence of nezukol in I. rubescens leaf tissue. The proposed IrTPS2-catalyzed reaction mechanism proceeds via the common ionization of the diphosphate group of (+)-CPP, followed by formation of an intermediary pimar-15-en-8-yl+ carbocation and neutralization of the carbocation by water capture at C-8 to yield nezukol, as confirmed by nuclear magnetic resonance (NMR) analysis. Oxygenation activity is rare for the family of class I diTPSs and offers new catalysts for developing metabolic engineering platforms to produce a broader spectrum of bioactive diterpenoid natural products.
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Affiliation(s)
- Kyle A. Pelot
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| | - Lynne M. Hagelthorn
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
| | - J. Bennett Addison
- Department of Chemistry, University of California-Davis, Davis, California, United States of America
| | - Philipp Zerbe
- Department of Plant Biology, University of California-Davis, Davis, California, United States of America
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18
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Nett RS, Contreras T, Peters RJ. Characterization of CYP115 As a Gibberellin 3-Oxidase Indicates That Certain Rhizobia Can Produce Bioactive Gibberellin A 4. ACS Chem Biol 2017; 12:912-917. [PMID: 28199080 PMCID: PMC5404427 DOI: 10.1021/acschembio.6b01038] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The
gibberellin (GA) phytohormones are produced not only by plants
but also by fungi and bacteria. Previous characterization of a cytochrome
P450 (CYP)-rich GA biosynthetic operon found in many symbiotic, nitrogen-fixing
rhizobia led to the elucidation of bacterial GA biosynthesis and implicated
GA9 as the final product. However, GA9 does
not exhibit hormonal/biological activity and presumably requires further
transformation to elicit an effect in the legume host plant. Some
rhizobia that contain the GA operon also possess an additional CYP
(CYP115), and here we show that this acts as a GA 3-oxidase to produce
bioactive GA4 from GA9. This is the first GA
3-oxidase identified for rhizobia, and provides a more complete scheme
for biosynthesis of bioactive GAs in bacteria. Furthermore, phylogenetic
analyses suggest that rhizobia acquired CYP115 independently of the
core GA operon, adding further complexity to the horizontal gene transfer
of GA biosynthetic enzymes among bacteria.
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Affiliation(s)
- Ryan S. Nett
- Roy
J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Tiffany Contreras
- Roy
J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
| | - Reuben J. Peters
- Roy
J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa 50011, United States
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19
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Nagel R, Peters RJ. Investigating the Phylogenetic Range of Gibberellin Biosynthesis in Bacteria. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2017; 30:343-349. [PMID: 28425831 PMCID: PMC5505637 DOI: 10.1094/mpmi-01-17-0001-r] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Certain plant-associated microbes can produce gibberellin (GA) phytohormones, as first described for the rice fungal pathogen Gibberella fujikuroi and, more recently, for bacteria, including several rhizobia and the rice bacterial pathogen Xanthomonas oryzae pv. oryzicola. The relevant enzymes are encoded by a biosynthetic operon that exhibits both a greater phylogenetic range and scattered distribution among plant-associated bacteria. Here, the phylogenetic distribution of this operon was investigated. To demonstrate conserved functionality, the enzymes encoded by the disparate operon from X. translucens pv. translucens, along with those from the most divergent example, found in Erwinia tracheiphila, were biochemically characterized. In both of these phytopathogens, the operon leads to production of the bioactive GA4. Based on these results, it seems that this operon is widely dedicated to GA biosynthesis. However, there is intriguing variation in the exact product. In particular, although all plant pathogens seem to produce bioactive GA4, rhizobia generally only produce the penultimate hormonal precursor GA9. This is suggested to reflect their distinct interactions with plants, because production of GA4 counteracts the jasmonic-acid-mediated defense response, reflecting the importance of wounds as the entry point for these phytopathogens, whereas such suppression presumably is detrimental in the rhizobial symbiotic relationship.
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Affiliation(s)
- Raimund Nagel
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, 1210 Molecular Biology Building, Ames 50011, U.S.A
| | - Reuben J Peters
- Iowa State University, Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, 1210 Molecular Biology Building, Ames 50011, U.S.A
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20
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Nagel R, Peters RJ. 18O2 labeling experiments illuminate the oxidation of ent-kaurene in bacterial gibberellin biosynthesis. Org Biomol Chem 2017; 15:7566-7571. [DOI: 10.1039/c7ob01819c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Parallel mechanisms between independently evolved plant and bacterial ent-kaurene oxidases.
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Affiliation(s)
- Raimund Nagel
- Roy J. Carver Department of Biochemistry
- Biophysics
- and Molecular Biology
- Iowa State University
- Ames
| | - Reuben J. Peters
- Roy J. Carver Department of Biochemistry
- Biophysics
- and Molecular Biology
- Iowa State University
- Ames
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21
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Mangwanda R, Zwart L, van der Merwe NA, Moleleki LN, Berger DK, Myburg AA, Naidoo S. Localization and Transcriptional Responses of Chrysoporthe austroafricana in Eucalyptus grandis Identify Putative Pathogenicity Factors. Front Microbiol 2016; 7:1953. [PMID: 28008326 PMCID: PMC5143476 DOI: 10.3389/fmicb.2016.01953] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 11/21/2016] [Indexed: 12/18/2022] Open
Abstract
Chrysoporthe austroafricana is a fungal pathogen that causes the development of stem cankers on susceptible Eucalyptus grandis trees. Clones of E. grandis that are partially resistant and highly susceptible have been identified based on the extent of lesion formation on the stem upon inoculation with C. austroafricana. These interactions have been used as a model pathosystem to enhance our understanding of interactions between pathogenic fungi and woody hosts, which may be different to herbaceous hosts. In previous research, transcriptomics of host responses in these two clones to C. austroafricana suggested roles for salicylic acid and gibberellic acid phytohormone signaling in defense. However, it is unclear how the pathogen infiltrates host tissue and which pathogenicity factors facilitate its spread in the two host genotypes. The aim of this study was to investigate these two aspects of the E. grandis-C. austroafricana interaction and to test the hypothesis that the pathogen possesses mechanisms to modulate the tree phytohormone-mediated defenses. Light microscopy showed that the pathogen occurred in most cell types and structures within infected E. grandis stem tissue. Notably, the fungus appeared to spread through the stem by penetrating cell wall pits. In order to understand the molecular interaction between these organisms and predict putative pathogenicity mechanisms of C. austroafricana, fungal gene expression was studied in vitro and in planta. Fungal genes associated with cell wall degradation, carbohydrate metabolism and phytohormone manipulation were expressed in planta by C. austroafricana. These genes could be involved in fungal spread by facilitating cell wall pit degradation and manipulating phytohormone mediated defense in each host environment, respectively. Specifically, the in planta expression of an ent-kaurene oxidase and salicylate hydroxylase in C. austroafricana suggests putative mechanisms by which the pathogen can modulate the phytohormone-mediated defenses of the host. These mechanisms have been reported in herbaceous plant-pathogen interactions, supporting the notion that these aspects of the interaction are similar in a woody species. This study highlights ent-kaurene oxidase and salicylate hydroxylase as candidates for further functional characterization.
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Affiliation(s)
- Ronishree Mangwanda
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Lizahn Zwart
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Nicolaas A. van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Lucy Novungayo Moleleki
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
| | - Dave Kenneth Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Alexander A. Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
| | - Sanushka Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute, Genomics Research Institute, University of PretoriaPretoria, South Africa
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22
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Jia M, Peters RJ. Extending a Single Residue Switch for Abbreviating Catalysis in Plant ent-Kaurene Synthases. FRONTIERS IN PLANT SCIENCE 2016; 7:1765. [PMID: 27920791 PMCID: PMC5118566 DOI: 10.3389/fpls.2016.01765] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/09/2016] [Indexed: 05/23/2023]
Abstract
Production of ent-kaurene as a precursor for important signaling molecules such as the gibberellins seems to have arisen early in plant evolution, with corresponding cyclase(s) present in all land plants (i.e., embryophyta). The relevant enzymes seem to represent fusion of the class II diterpene cyclase that produces the intermediate ent-copalyl diphosphate (ent-CPP) and the subsequently acting class I diterpene synthase that produces ent-kaurene, although the bifunctionality of the ancestral gene is only retained in certain early diverging plants, with gene duplication and sub-functionalization leading to distinct ent-CPP synthases and ent-kaurene synthases (KSs) generally observed. This evolutionary scenario implies that plant KSs should have conserved structural features uniquely required for production of ent-kaurene relative to related enzymes that have alternative function. Notably, substitution of threonine for a conserved isoleucine has been shown to "short-circuit" the complex bicyclization and rearrangement reaction catalyzed by KSs after initial cyclization, leading to predominant production of ent-pimaradiene, at least in KSs from angiosperms. Here this effect is shown to extend to KSs from earlier diverging plants (i.e., bryophytes), including a bifunctional/KS. In addition, attribution of the dramatic effect of this single residue "switch" on product outcome to electrostatic stabilization of the ent-pimarenyl carbocation intermediate formed upon initial cyclization by the hydroxyl introduced by threonine substitution has been called into question by the observation of similar effects from substitution of alanine. Here further mutational analysis and detailed product analysis is reported that supports the importance of electrostatic stabilization by a hydroxyl or water.
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Nett RS, Montanares M, Marcassa A, Lu X, Nagel R, Charles TC, Hedden P, Rojas MC, Peters RJ. Elucidation of gibberellin biosynthesis in bacteria reveals convergent evolution. Nat Chem Biol 2016; 13:69-74. [PMID: 27842068 DOI: 10.1038/nchembio.2232] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 09/23/2016] [Indexed: 12/22/2022]
Abstract
Gibberellins (GAs) are crucial phytohormones involved in many aspects of plant growth and development, including plant-microbe interactions, which has led to GA production by plant-associated fungi and bacteria as well. While the GA biosynthetic pathways in plants and fungi have been elucidated and found to have arisen independently through convergent evolution, little has been uncovered about GA biosynthesis in bacteria. Some nitrogen-fixing, symbiotic, legume-associated rhizobia, including Bradyrhizobium japonicum-the symbiont of soybean-and Sinorhizobium fredii-a broad-host-nodulating species-contain a putative GA biosynthetic operon, or gene cluster. Through functional characterization of five unknown genes, we demonstrate that this operon encodes the enzymes necessary to produce GA9, thereby elucidating bacterial GA biosynthesis. The distinct nature of these enzymes indicates that bacteria have independently evolved a third biosynthetic pathway for GA production. Furthermore, our results also reveal a central biochemical logic that is followed in all three convergently evolved GA biosynthetic pathways.
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Affiliation(s)
- Ryan S Nett
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Mariana Montanares
- Laboratorio de Bioorgánica, Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ariana Marcassa
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Xuan Lu
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Raimund Nagel
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Peter Hedden
- Rothamsted Research, Harpenden, Hertfordshire, UK
| | - Maria Cecilia Rojas
- Laboratorio de Bioorgánica, Departamento de Química, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, Iowa, USA
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Jia M, Potter KC, Peters RJ. Extreme promiscuity of a bacterial and a plant diterpene synthase enables combinatorial biosynthesis. Metab Eng 2016; 37:24-34. [PMID: 27060773 DOI: 10.1016/j.ymben.2016.04.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 03/25/2016] [Accepted: 04/06/2016] [Indexed: 11/30/2022]
Abstract
Diterpenes are widely distributed across many biological kingdoms, where they serve a diverse range of physiological functions, and some have significant industrial utility. Their biosynthesis involves class I diterpene synthases (DTSs), whose activity can be preceded by that of class II diterpene cyclases (DTCs). Here, a modular metabolic engineering system was used to examine the promiscuity of DTSs. Strikingly, both a bacterial and plant DTS were found to exhibit extreme promiscuity, reacting with all available precursors with orthogonal activity, producing an olefin or hydroxyl group, respectively. Such DTS promiscuity enables combinatorial biosynthesis, with remarkably high yields for these unoptimized non-native enzymatic combinations (up to 15mg/L). Indeed, it was possible to readily characterize the 13 unknown products. Notably, 16 of the observed diterpenes were previously inaccessible, and these results provide biosynthetic routes that are further expected to enable assembly of more extended pathways to produce additionally elaborated 'non-natural' diterpenoids.
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Affiliation(s)
- Meirong Jia
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Kevin C Potter
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Reuben J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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Mafu S, Potter KC, Hillwig ML, Schulte S, Criswell J, Peters RJ. Efficient heterocyclisation by (di)terpene synthases. Chem Commun (Camb) 2015; 51:13485-13487. [PMID: 26214384 PMCID: PMC4543578 DOI: 10.1039/c5cc05754j] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
While cyclic ether forming terpene synthases are known, the basis for such heterocyclisation is unclear. Here it is reported that numerous (di)terpene synthases, particularly including the ancestral ent-kaurene synthase, efficiently produce isomers of manoyl oxide from the stereochemically appropriate substrate. Accordingly, such heterocyclisation is easily accomplished by terpene synthases. Indeed, the use of single residue changes to induce production of the appropriate substrate in the upstream active site leads to efficient bifunctional enzymes producing isomers of manoyl oxide, representing novel enzymatic activity.
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Affiliation(s)
- S Mafu
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - K C Potter
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - M L Hillwig
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - S Schulte
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - J Criswell
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
| | - R J Peters
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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