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Song S, Morales Moreira Z, Briggs AL, Zhang XC, Diener AC, Haney CH. PSKR1 balances the plant growth-defence trade-off in the rhizosphere microbiome. NATURE PLANTS 2023; 9:2071-2084. [PMID: 37973937 DOI: 10.1038/s41477-023-01539-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 09/08/2023] [Indexed: 11/19/2023]
Abstract
Microbiota benefit their hosts by improving nutrient uptake and pathogen protection. How host immunity restricts microbiota while avoiding autoimmunity is poorly understood. Here we show that the Arabidopsis phytosulfokine receptor 1 (pskr1) mutant displays autoimmunity (plant stunting, defence-gene expression and reduced rhizosphere bacterial growth) in response to growth-promoting Pseudomonas fluorescens. Microbiome profiling and microbiota colonization showed that PSKR1-mediated reduction in bacterial growth and stunting is largely specific to Pseudomonas. Transcriptional profiling demonstrated that PSKR1 regulates the growth-defence trade-off during Pseudomonas colonization: PSKR1 upregulates plant photosynthesis and root growth but suppresses salicylic-acid-mediated defences. Genetic epistasis experiments showed that pskr1 stunting and restriction of bacterial growth are salicylic acid dependent. Finally, we showed that Pseudomonas, but not other bacteria, induces PSKR1 expression in roots, suggesting that Pseudomonas might manipulate plant signalling to promote its colonization. Our data demonstrate a genetic mechanism to coordinate beneficial functions of the microbiome while preventing autoimmunity.
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Affiliation(s)
- Siyu Song
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zayda Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Annika L Briggs
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xue-Cheng Zhang
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Andrew C Diener
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Biological Sciences, The University of Pittsburgh, Pittsburgh, PA, USA.
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2
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A Genome-Wide Screen Identifies Genes in Rhizosphere-Associated Pseudomonas Required to Evade Plant Defenses. mBio 2018; 9:mBio.00433-18. [PMID: 30401768 PMCID: PMC6222131 DOI: 10.1128/mbio.00433-18] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
While rhizosphere bacteria hold the potential to improve plant health and fitness, little is known about the bacterial genes required to evade host immunity. Using a model system consisting of Arabidopsis and a beneficial Pseudomonas sp. isolate, we identified bacterial genes required for both rhizosphere fitness and for evading host immune responses. This work advances our understanding of how evasion of host defenses contributes to survival in the rhizosphere. Pseudomonas fluorescens and related plant root (“rhizosphere”)-associated species contribute to plant health by modulating defenses and facilitating nutrient uptake. To identify bacterial fitness determinants in the rhizosphere of the model plant Arabidopsis thaliana, we performed a high-throughput transposon sequencing (Tn-Seq) screen using the biocontrol and growth-promoting strain Pseudomonas sp. WCS365. The screen, which was performed in parallel on wild-type and immunocompromised Arabidopsis plants, identified 231 genes that increased fitness in the rhizosphere of wild-type plants. A subset of these genes decreased fitness in the rhizosphere of immunocompromised plants. We hypothesized that these genes might be involved in avoiding plant defenses and verified 7 Pseudomonas sp. WCS365 candidate genes by generating clean deletions. We found that two of these deletion mutants, ΔmorA (encoding a putative diguanylate cyclase/phosphodiesterase) and ΔspuC (encoding a putrescine aminotransferase), formed enhanced biofilms and inhibited plant growth. We found that mutants ΔspuC and ΔmorA induced pattern-triggered immunity (PTI) as measured by induction of an Arabidopsis PTI reporter and FLS2/BAK1-dependent inhibition of plant growth. We show that MorA acts as a phosphodiesterase to inhibit biofilm formation, suggesting a possible role in biofilm dispersal. We found that both putrescine and its precursor arginine promote biofilm formation that is enhanced in the ΔspuC mutant, which cannot break down putrescine, suggesting that putrescine might serve as a signaling molecule in the rhizosphere. Collectively, this work identified novel bacterial factors required to evade plant defenses in the rhizosphere.
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3
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Haney CH, Wiesmann CL, Shapiro LR, Melnyk RA, O'Sullivan LR, Khorasani S, Xiao L, Han J, Bush J, Carrillo J, Pierce NE, Ausubel FM. Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens. Mol Ecol 2017; 27:1833-1847. [PMID: 29087012 DOI: 10.1111/mec.14400] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/18/2017] [Accepted: 10/19/2017] [Indexed: 01/02/2023]
Abstract
Plant-associated soil microbes are important mediators of plant defence responses to diverse above-ground pathogen and insect challengers. For example, closely related strains of beneficial rhizosphere Pseudomonas spp. can induce systemic resistance (ISR), systemic susceptibility (ISS) or neither against the bacterial foliar pathogen Pseudomonas syringae pv. tomato DC3000 (Pto DC3000). Using a model system composed of root-associated Pseudomonas spp. strains, the foliar pathogen Pto DC3000 and the herbivore Trichoplusia ni (cabbage looper), we found that rhizosphere-associated Pseudomonas spp. that induce either ISS and ISR against Pto DC3000 all increased resistance to herbivory by T. ni. We found that resistance to T. ni and resistance to Pto DC3000 are quantitative metrics of the jasmonic acid (JA)/salicylic acid (SA) trade-off and distinct strains of rhizosphere-associated Pseudomonas spp. have distinct effects on the JA/SA trade-off. Using genetic analysis and transcriptional profiling, we provide evidence that treatment of Arabidopsis with Pseudomonas sp. CH267, which induces ISS against bacterial pathogens, tips the JA/SA trade-off towards JA-dependent defences against herbivores at the cost of a subset of SA-mediated defences against bacterial pathogens. In contrast, treatment of Arabidopsis with the ISR strain Pseudomonas sp. WCS417 disrupts JA/SA antagonism and simultaneously primes plants for both JA- and SA-mediated defences. Our findings show that ISS against the bacterial foliar pathogens triggered by Pseudomonas sp. CH267, which is a seemingly deleterious phenotype, may in fact be an adaptive consequence of increased resistance to herbivory. Our work shows that pleiotropic effects of microbiome modulation of plant defences are important to consider when using microbes to modify plant traits in agriculture.
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Affiliation(s)
- Cara H Haney
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada.,Michael Smith Laboratories, The University of British Columbia, Vancouver, BC, Canada
| | - Christina L Wiesmann
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Lori R Shapiro
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, USA.,Department of Applied Ecology, North Carolina State University, Raleigh, NC, USA
| | - Ryan A Melnyk
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Lucy R O'Sullivan
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Sophie Khorasani
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Li Xiao
- Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada.,Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Jiatong Han
- Department of Microbiology and Immunology, The University of British Columbia, Vancouver, BC, Canada
| | - Jenifer Bush
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Juli Carrillo
- Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Frederick M Ausubel
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA.,Department of Genetics, Harvard Medical School, Boston, MA, USA
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4
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Campbell BW, Hofstad AN, Sreekanta S, Fu F, Kono TJY, O'Rourke JA, Vance CP, Muehlbauer GJ, Stupar RM. Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1725-38. [PMID: 27282876 PMCID: PMC4983299 DOI: 10.1007/s00122-016-2735-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/28/2016] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Three adjacent and distinct sequence rearrangements were identified at a NAP1 locus in a soybean mutant. Genetic dissection and validation revealed the function of this gene in soybean trichome development. A soybean (Glycine max (L.) Merr.) gnarled trichome mutant, exhibiting stunted trichomes compared to wild-type, was identified in a fast neutron mutant population. Genetic mapping using whole genome sequencing-based bulked segregant analysis identified a 26.6 megabase interval on chromosome 20 that co-segregated with the phenotype. Comparative genomic hybridization analysis of the mutant indicated that the chromosome 20 interval included a small structural variant within the coding region of a soybean ortholog (Glyma.20G019300) of Arabidopsis Nck-Associated Protein 1 (NAP1), a regulator of actin nucleation during trichome morphogenesis. Sequence analysis of the candidate allele revealed multiple rearrangements within the coding region, including two deletions (approximately 1-2 kb each), a translocation, and an inversion. Further analyses revealed that the mutant allele perfectly co-segregated with the phenotype, and a wild-type soybean NAP1 transgene functionally complemented an Arabidopsis nap1 mutant. In addition, mapping and exon sequencing of NAP1 in a spontaneous soybean gnarled trichome mutant (T31) identified a frame shift mutation resulting in a truncation of the coding region. These data indicate that the soybean NAP1 gene is essential for proper trichome development and show the utility of the soybean fast neutron population for forward genetic approaches for identifying genes.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Anna N Hofstad
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Suma Sreekanta
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Fengli Fu
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Thomas J Y Kono
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Jamie A O'Rourke
- USDA-ARS, Corn Insects and Crop Genetics Research, Iowa State University, Ames, IA, 50011, USA
| | - Carroll P Vance
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA
- Department of Plant Biology, University of Minnesota, Saint Paul, MN, 55108, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN, 55108, USA.
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5
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Shakeel T, Fatma Z, Fatma T, Yazdani SS. Heterogeneity of alkane chain length in freshwater and marine cyanobacteria. Front Bioeng Biotechnol 2015; 3:34. [PMID: 25853127 PMCID: PMC4360714 DOI: 10.3389/fbioe.2015.00034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 03/02/2015] [Indexed: 11/25/2022] Open
Abstract
The potential utilization of cyanobacteria for the biological production of alkanes represents an exceptional system for the next generation of biofuels. Here, we analyzed a diverse group of freshwater and marine cyanobacterial isolates from Indian culture collections for their ability to produce both alkanes and alkenes. Among the 50 cyanobacterial isolates screened, 32 isolates; 14 freshwater and 18 marine isolates; produced predominantly alkanes. The GC-MS/MS profiles revealed a higher percentage of pentadecane and heptadecane production for marine and freshwater strains, respectively. Oscillatoria species were found to be the highest producers of alkanes. Among the freshwater isolates, Oscillatoria CCC305 produced the maximum alkane level with 0.43 μg/mg dry cell weight, while Oscillatoria formosa BDU30603 was the highest producer among the marine isolates with 0.13 μg/mg dry cell weight. Culturing these strains under different media compositions showed that the alkane chain length was not influenced by the growth medium but was rather an inherent property of the strains. Analysis of the cellular fatty acid content indicated the presence of predominantly C16 chain length fatty acids in marine strains, while the proportion of C18 chain length fatty acids increased in the majority of freshwater strains. These results correlated with alkane chain length specificity of marine and freshwater isolates indicating that alkane chain lengths may be primarily determined by the fatty acid synthesis pathway. Moreover, the phylogenetic analysis showed clustering of pentadecane-producing marine strains that was distinct from heptadecane-producing freshwater strains strongly suggesting a close association between alkane chain length and the cyanobacteria habitat.
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Affiliation(s)
- Tabinda Shakeel
- Synthetic Biology and Biofuels Group, International Centre for Genetic Engineering and Biotechnology , New Delhi , India
| | - Zia Fatma
- Synthetic Biology and Biofuels Group, International Centre for Genetic Engineering and Biotechnology , New Delhi , India
| | - Tasneem Fatma
- Department of Biosciences, Jamia Millia Islamia , New Delhi , India
| | - Syed Shams Yazdani
- Synthetic Biology and Biofuels Group, International Centre for Genetic Engineering and Biotechnology , New Delhi , India ; DBT-ICGEB Centre for Advanced Bioenergy Research, International Centre for Genetic Engineering and Biotechnology , New Delhi , India
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6
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Zhang XC, Millet YA, Cheng Z, Bush J, Ausubel FM. Jasmonate signalling in Arabidopsis involves SGT1b-HSP70-HSP90 chaperone complexes. NATURE PLANTS 2015; 1:15049. [PMID: 27054042 PMCID: PMC4819967 DOI: 10.1038/nplants.2015.49] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 03/23/2015] [Indexed: 05/20/2023]
Abstract
Plant hormones play pivotal roles in growth, development and stress responses. Although it is essential to our understanding of hormone signalling, how plants maintain a steady state level of hormone receptors is poorly understood. We show that mutation of the Arabidopsis thaliana co-chaperone SGT1b impairs responses to the plant hormones jasmonate, auxin and gibberellic acid, but not brassinolide and abscisic acid, and that SGT1b and its homologue SGT1a are involved in maintaining the steady state levels of the F-box proteins COI1 and TIR1, receptors for jasmonate and auxin, respectively. The association of SGT1b with COI1 is direct and is independent of the Arabidopsis SKP1 protein, ASK1. We further show that COI1 is a client protein of SGT1b-HSP70-HSP90 chaperone complexes and that the complexes function in hormone signalling by stabilizing the COI1 protein. This study extends the SGT1b-HSP90 client protein list and broadens the functional scope of SGT1b-HSP70-HSP90 chaperone complexes.
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Affiliation(s)
- Xue-Cheng Zhang
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Yves A. Millet
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Zhenyu Cheng
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Jenifer Bush
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Frederick M. Ausubel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
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