1
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Wilkinson H, Coppock A, Richmond BL, Lagunas B, Gifford ML. Plant-Environment Response Pathway Regulation Uncovered by Investigating Non-Typical Legume Symbiosis and Nodulation. PLANTS (BASEL, SWITZERLAND) 2023; 12:1964. [PMID: 37653881 PMCID: PMC10223263 DOI: 10.3390/plants12101964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Nitrogen is an essential element needed for plants to survive, and legumes are well known to recruit rhizobia to fix atmospheric nitrogen. In this widely studied symbiosis, legumes develop specific structures on the roots to host specific symbionts. This review explores alternate nodule structures and their functions outside of the more widely studied legume-rhizobial symbiosis, as well as discussing other unusual aspects of nodulation. This includes actinorhizal-Frankia, cycad-cyanobacteria, and the non-legume Parasponia andersonii-rhizobia symbioses. Nodules are also not restricted to the roots, either, with examples found within stems and leaves. Recent research has shown that legume-rhizobia nodulation brings a great many other benefits, some direct and some indirect. Rhizobial symbiosis can lead to modifications in other pathways, including the priming of defence responses, and to modulated or enhanced resistance to biotic and abiotic stress. With so many avenues to explore, this review discusses recent discoveries and highlights future directions in the study of nodulation.
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Affiliation(s)
- Helen Wilkinson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Alice Coppock
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | | | - Beatriz Lagunas
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Miriam L. Gifford
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Warwick Integrative Synthetic Biology Centre, University of Warwick, Coventry CV4 7AL, UK
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2
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Danneels B, Blignaut M, Marti G, Sieber S, Vandamme P, Meyer M, Carlier A. Cyclitol metabolism is a central feature of Burkholderia leaf symbionts. Environ Microbiol 2023; 25:454-472. [PMID: 36451580 DOI: 10.1111/1462-2920.16292] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 11/28/2022] [Indexed: 12/03/2022]
Abstract
The symbioses between plants of the Rubiaceae and Primulaceae families with Burkholderia bacteria represent unique and intimate plant-bacterial relationships. Many of these interactions have been identified through PCR-dependent typing methods, but there is little information available about their functional and ecological roles. We assembled 17 new endophyte genomes representing endophytes from 13 plant species, including those of two previously unknown associations. Genomes of leaf endophytes belonging to Burkholderia s.l. show extensive signs of genome reduction, albeit to varying degrees. Except for one endophyte, none of the bacterial symbionts could be isolated on standard microbiological media. Despite their taxonomic diversity, all endophyte genomes contained gene clusters linked to the production of specialized metabolites, including genes linked to cyclitol sugar analog metabolism and in one instance non-ribosomal peptide synthesis. These genes and gene clusters are unique within Burkholderia s.l. and are likely horizontally acquired. We propose that the acquisition of secondary metabolite gene clusters through horizontal gene transfer is a prerequisite for the evolution of a stable association between these endophytes and their hosts.
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Affiliation(s)
- Bram Danneels
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- Computational Biology Unit, Department of Informatics, University of Bergen, Norway
| | - Monique Blignaut
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Guillaume Marti
- Metatoul-AgromiX Platform, LRSV, Université de Toulouse, CNRS, UT3, INP, Toulouse, France
- MetaboHUB-MetaToul, National Infrastructure of Metabolomics and Fluxomics, Toulouse, France
| | - Simon Sieber
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Peter Vandamme
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Marion Meyer
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
| | - Aurélien Carlier
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
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3
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Georgiou A, Sieber S, Hsiao CC, Grayfer T, Gorenflos López JL, Gademann K, Eberl L, Bailly A. Leaf nodule endosymbiotic Burkholderia confer targeted allelopathy to their Psychotria hosts. Sci Rep 2021; 11:22465. [PMID: 34789815 PMCID: PMC8599487 DOI: 10.1038/s41598-021-01867-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/03/2021] [Indexed: 11/11/2022] Open
Abstract
After a century of investigations, the function of the obligate betaproteobacterial endosymbionts accommodated in leaf nodules of tropical Rubiaceae remained enigmatic. We report that the α-D-glucose analogue (+)-streptol, systemically supplied by mature Ca. Burkholderia kirkii nodules to their Psychotria hosts, exhibits potent and selective root growth inhibiting activity. We provide compelling evidence that (+)-streptol specifically affects meristematic root cells transitioning to anisotropic elongation by disrupting cell wall organization in a mechanism of action that is distinct from canonical cellulose biosynthesis inhibitors. We observed no inhibitory or cytotoxic effects on organisms other than seed plants, further suggesting (+)-streptol as a bona fide allelochemical. We propose that the suppression of growth of plant competitors is a major driver of the formation and maintenance of the Psychotria-Burkholderia association. In addition to potential agricultural applications as a herbicidal agent, (+)-streptol might also prove useful to dissect plant cell and organ growth processes.
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Affiliation(s)
- Antri Georgiou
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Chien-Chi Hsiao
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Tatyana Grayfer
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jacob L Gorenflos López
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Leo Eberl
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
| | - Aurélien Bailly
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland.
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4
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Schindler F, Fragner L, Herpell JB, Berger A, Brenner M, Tischler S, Bellaire A, Schönenberger J, Li W, Sun X, Schinnerl J, Brecker L, Weckwerth W. Dissecting Metabolism of Leaf Nodules in Ardisia crenata and Psychotria punctata. Front Mol Biosci 2021; 8:683671. [PMID: 34395523 PMCID: PMC8362603 DOI: 10.3389/fmolb.2021.683671] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 06/29/2021] [Indexed: 11/13/2022] Open
Abstract
Root-microbe interaction and its specialized root nodule structures and functions are well studied. In contrast, leaf nodules harboring microbial endophytes in special glandular leaf structures have only recently gained increased interest as plant-microbe phyllosphere interactions. Here, we applied a comprehensive metabolomics platform in combination with natural product isolation and characterization to dissect leaf and leaf nodule metabolism and functions in Ardisia crenata (Primulaceae) and Psychotria punctata (Rubiaceae). The results indicate that abiotic stress resilience plays an important part within the leaf nodule symbiosis of both species. Both species showed metabolic signatures of enhanced nitrogen assimilation/dissimilation pattern and increased polyamine levels in nodules compared to leaf lamina tissue potentially involved in senescence processes and photosynthesis. Multiple links to cytokinin and REDOX-active pathways were found. Our results further demonstrate that secondary metabolite production by endophytes is a key feature of this symbiotic system. Multiple anhydromuropeptides (AhMP) and their derivatives were identified as highly characteristic biomarkers for nodulation within both species. A novel epicatechin derivative was structurally elucidated with NMR and shown to be enriched within the leaf nodules of A. crenata. This enrichment within nodulated tissues was also observed for catechin and other flavonoids indicating that flavonoid metabolism may play an important role for leaf nodule symbiosis of A. crenata. In contrast, pavettamine was only detected in P. punctata and showed no nodule specific enrichment but a developmental effect. Further natural products were detected, including three putative unknown depsipeptide structures in A. crenata leaf nodules. The analysis presents a first metabolomics reference data set for the intimate interaction of microbes and plants in leaf nodules, reveals novel metabolic processes of plant-microbe interaction as well as the potential of natural product discovery in these systems.
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Affiliation(s)
- Florian Schindler
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Lena Fragner
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Johannes B Herpell
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Andreas Berger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Martin Brenner
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria.,Department of Pharmaceutical Sciences/Pharmacognosy, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Sonja Tischler
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Anke Bellaire
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Weimin Li
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Xiaoliang Sun
- Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Johann Schinnerl
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Lothar Brecker
- Department of Organic Chemistry, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology (MOSYS), Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
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5
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Sieber S, Hsiao CC, Emmanouilidou D, Debowski AW, Stubbs KA, Gademann K. Syntheses and biological investigations of kirkamide and oseltamivir hybrid derivatives. Tetrahedron 2020. [DOI: 10.1016/j.tet.2020.131386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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6
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Varadarajan AR, Goetze S, Pavlou MP, Grosboillot V, Shen Y, Loessner MJ, Ahrens CH, Wollscheid B. A Proteogenomic Resource Enabling Integrated Analysis of Listeria Genotype-Proteotype-Phenotype Relationships. J Proteome Res 2020; 19:1647-1662. [PMID: 32091902 DOI: 10.1021/acs.jproteome.9b00842] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Listeria monocytogenes is an opportunistic foodborne pathogen responsible for listeriosis, a potentially fatal foodborne disease. Many different Listeria strains and serotypes exist, but a proteogenomic resource that bridges the gap in our molecular understanding of the relationships between the Listeria genotypes and phenotypes via proteotypes is still missing. Here, we devised a next-generation proteogenomics strategy that enables the community to rapidly proteotype Listeria strains and relate this information back to the genotype. Based on sequencing and de novo assembly of the two most commonly used Listeria model strains, EGD-e and ScottA, we established two comprehensive Listeria proteogenomic databases. A genome comparison established core- and strain-specific genes potentially responsible for virulence differences. Next, we established a DIA/SWATH-based proteotyping strategy, including a new and robust sample preparation workflow, that enables the reproducible, sensitive, and relative quantitative measurement of Listeria proteotypes. This reusable and publicly available DIA/SWATH library covers 70% of open reading frames of Listeria and represents the most extensive spectral library for Listeria proteotype analysis to date. We used these two new resources to investigate the Listeria proteotype in states mimicking the upper gastrointestinal passage. Exposure of Listeria to bile salts at 37 °C, which simulates conditions encountered in the duodenum, showed significant proteotype perturbations including an increase of FlaA, the structural protein of flagella. Given that Listeria is known to lose its flagella above 30 °C, this was an unexpected finding. The formation of flagella, which might have implications on infectivity, was validated by parallel reaction monitoring and light and scanning electron microscopy. flaA transcript levels did not change significantly upon exposure to bile salts at 37 °C, suggesting regulation at the post-transcriptional level. Together, these analyses provide a comprehensive proteogenomic resource and toolbox for the Listeria community enabling the analysis of Listeria genotype-proteotype-phenotype relationships.
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Affiliation(s)
- Adithi R Varadarajan
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, 8820 Wädenswil, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
| | - Maria P Pavlou
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
| | - Virginie Grosboillot
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Yang Shen
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Martin J Loessner
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Institute of Food, Nutrition and Health (IFNH), ETH Zürich, 8092 Zürich, Switzerland
| | - Christian H Ahrens
- Agroscope, Molecular Diagnostics, Genomics & Bioinformatics, 8820 Wädenswil, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology (D-HEST), ETH Zürich, 8092 Zürich, Switzerland.,Swiss Institute of Bioinformatics (SIB), 1015 Lausanne, Switzerland.,Institute of Translational Medicine (ITM), ETH Zürich, 8093 Zürich, Switzerland
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7
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He W, Megharaj M, Wu CY, Subashchandrabose SR, Dai CC. Endophyte-assisted phytoremediation: mechanisms and current application strategies for soil mixed pollutants. Crit Rev Biotechnol 2019; 40:31-45. [PMID: 31656090 DOI: 10.1080/07388551.2019.1675582] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phytoremediation uses plants and associated microbes to remove pollutants from the environment and is considered a promising bioremediation method. Compared with well-described single contaminant treatments, the number of studies reporting phytoremediation of soil mixed pollutants has increased recently. Endophytes, including bacteria and fungi, exhibit beneficial traits for the promotion of plant growth, stress alleviation, and biodegradation. Moreover, endophytes either directly or indirectly assist host plants to survive high concentrations of organic and inorganic pollutants in the soil. Endophytic microorganisms can also regulate the plant metabolism in different ways, exhibiting a variety of physiological characteristics. This review summarizes the taxa and physiological properties of endophytic microorganisms that may participate in the detoxification of contaminant mixtures. Furthermore, potential biomolecules that may enhance endophyte mediated phytoremediation are discussed. The practical applications of pollutant-degrading endophytes and current strategies for applying this valuable bio-resource to soil phytoremediation are summarized.
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Affiliation(s)
- Wei He
- College of Life Sciences, Nanjing Normal University, Nanjing, China.,Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Mallavarapu Megharaj
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Chun-Ya Wu
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Suresh R Subashchandrabose
- Global Centre for Environmental Remediation (GCER), The University of Newcastle (UoN), Callaghan, Australia
| | - Chuan-Chao Dai
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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8
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Sinnesael A, Leroux O, Janssens SB, Smets E, Panis B, Verstraete B. Is the bacterial leaf nodule symbiosis obligate for Psychotria umbellata? The development of a Burkholderia-free host plant. PLoS One 2019; 14:e0219863. [PMID: 31310638 PMCID: PMC6634412 DOI: 10.1371/journal.pone.0219863] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 07/02/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND & AIMS The bacterial leaf nodule symbiosis is an interaction where bacteria are housed in specialised structures in the leaves of their plant host. In the Rubiaceae plant family, host plants interact with Burkholderia bacteria. This interaction might play a role in the host plant defence system. It is unique due to its high specificity; the vertical transmission of the endophyte to the next generation of the host plant; and its supposedly obligatory character. Although previous attempts have been made to investigate this obligatory character by developing Burkholderia-free plants, none have succeeded and nodulating plants were still produced. In order to investigate the obligatory character of this endosymbiosis, our aims were to develop Burkholderia-free Psychotria umbellata plants and to investigate the effect of the absence of the endophytes on the host in a controlled environment. METHODS The Burkholderia-free plants were obtained via embryo culture, a plant cultivation technique. In order to analyse the endophyte-free status, we screened the plants morphologically, microscopically and molecularly over a period of three years. To characterise the phenotype and growth of the in vitro aposymbiotic plants, we compared the growth of the Burkholderia-free plants to the nodulating plants under the same in vitro conditions. KEY RESULTS All the developed plants were Burkholderia-free and survived in a sterile in vitro environment. The growth analysis showed that plants without endophytes had a slower development. CONCLUSIONS Embryo culture is a cultivation technique with a high success rate for the development of Burkholderia-free plants of P. umbellata. The increased growth rate in vitro when the specific endophyte is present cannot be explained by possible benefits put forward in previous studies. This might indicate that the benefits of the endosymbiosis are not yet completely understood.
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Affiliation(s)
- Arne Sinnesael
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | | | - Steven B. Janssens
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Meise Botanic Garden, Meise, Belgium
| | - Erik Smets
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Naturalis Biodiversity Center, Leiden, the Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, the Netherlands
| | - Bart Panis
- Bioversity International, Leuven, Belgium
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9
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Adaptations and evolution of a heritable leaf nodule symbiosis between Dioscorea sansibarensis and Orrella dioscoreae. ISME JOURNAL 2019; 13:1831-1844. [PMID: 30877285 DOI: 10.1038/s41396-019-0398-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 03/05/2019] [Accepted: 03/05/2019] [Indexed: 12/31/2022]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves in what is commonly referred to as leaf nodule symbiosis. We describe here a highly specific symbiosis between a wild yam species from Madagascar, Dioscorea sansibarensis and bacteria of the species Orrella dioscoreae. Using whole-genome sequencing of plastids and bacteria from wild-collected samples, we show phylogenetic patterns consistent with a dominant vertical mode of transmission of the symbionts. Unique so far among leaf nodule symbioses, the bacteria can be cultured and are amenable to comparative transcriptomics, revealing a potential role in complementing the host's arsenal of secondary metabolites. We propose a recent establishment of a vertical mode of transmission in this symbiosis which, together with a large effective population size explains the cultivability and apparent lack of genome reductive evolution in O. dioscoreae. We leverage these unique features to reveal pathways and functions under positive selection in these specialized endophytes, highlighting the candidate mechanisms enabling a permanent association in the phyllosphere.
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10
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Hsiao CC, Sieber S, Georgiou A, Bailly A, Emmanouilidou D, Carlier A, Eberl L, Gademann K. Synthesis and Biological Evaluation of the Novel Growth Inhibitor Streptol Glucoside, Isolated from an Obligate Plant Symbiont. Chemistry 2019; 25:1722-1726. [PMID: 30508325 DOI: 10.1002/chem.201805693] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 11/29/2018] [Indexed: 12/23/2022]
Abstract
The plant Psychotria kirkii hosts an obligatory bacterial symbiont, Candidatus Burkholderia kirkii, in nodules on their leaves. Recently, a glucosylated derivative of (+)-streptol, (+)-streptol glucoside, was isolated from the nodulated leaves and was found to possess a plant growth inhibitory activity. To establish a structure-activity relationship study, a convergent strategy was developed to obtain several pseudosugars from a single synthetic precursor. Furthermore, the glucosylation of streptol was investigated in detail and conditions affording specifically the α or β glucosidic anomer were identified. Although (+)-streptol was the most active compound, its concentration in P. kirkii plant leaves extract was approximately ten-fold lower than that of (+)-streptol glucoside. These results provide compelling evidence that the glucosylation of (+)-streptol protects the plant host against the growth inhibitory effect of the compound, which might constitute a molecular cornerstone for this successful plant-bacteria symbiosis.
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Affiliation(s)
- Chien-Chi Hsiao
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Antri Georgiou
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Aurélien Bailly
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Despina Emmanouilidou
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Aurélien Carlier
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Leo Eberl
- Institute of Plant and Microbial Biology, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
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11
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Sinnesael A, Eeckhout S, Janssens SB, Smets E, Panis B, Leroux O, Verstraete B. Detection of Burkholderia in the seeds of Psychotria punctata (Rubiaceae) - Microscopic evidence for vertical transmission in the leaf nodule symbiosis. PLoS One 2018; 13:e0209091. [PMID: 30550604 PMCID: PMC6294375 DOI: 10.1371/journal.pone.0209091] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 11/29/2018] [Indexed: 11/25/2022] Open
Abstract
Background and aims The bacterial leaf nodule symbiosis is a close interaction between endophytes and their plant hosts, mainly within the coffee family. The interaction between Rubiaceae species and Burkholderia bacteria is unique due to its obligate nature, high specificity, and predominantly vertical transmission of the endophytes to the next generation of host plants. This vertical transmission is intriguing since it is the basis for the uniqueness of the symbiosis. However, unequivocal evidence of the location of the endophytes in the seeds is lacking. The aim of this paper is therefore to demonstrate the presence of the host specific endophyte in the seeds of Psychotria punctata and confirm its precise location. In addition, the suggested location of the endophyte in other parts of the host plant is investigated. Methods To identify and locate the endophyte in Psychotria punctata, a two-level approach was adopted using both a molecular screening method and fluorescent in situ hybridisation microscopy. Key results The endophytes, molecularly identified as Candidatus Burkholderia kirkii, were detected in the leaves, vegetative and flower buds, anthers, gynoecium, embryos, and young twigs. In addition, they were in situ localised in leaves, flowers and shoot apical meristems, and, for the first time, in between the cotyledons of the embryos. Conclusions Both independent techniques detected the host specific endophyte in close proximity to the shoot apical meristem of the embryo, which confirms for the first time the exact location of the endophytes in the seeds. This study provides reliable proof that the endophytes are maintained throughout the growth and development of the host plant and are transmitted vertically to the offspring.
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Affiliation(s)
- Arne Sinnesael
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Botanic Garden Meise, Meise, Belgium
- * E-mail:
| | | | | | - Erik Smets
- Plant Conservation and Population Biology, Department of Biology, KU Leuven, Leuven, Belgium
- Naturalis Biodiversity Center, University of Leiden, Leiden, the Netherlands
| | - Bart Panis
- Bioversity International, Leuven, Belgium
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12
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Danneels B, Pinto-Carbó M, Carlier A. Patterns of Nucleotide Deletion and Insertion Inferred from Bacterial Pseudogenes. Genome Biol Evol 2018; 10:1792-1802. [PMID: 29982456 PMCID: PMC6054270 DOI: 10.1093/gbe/evy140] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/29/2018] [Indexed: 02/06/2023] Open
Abstract
Pseudogenes are a paradigm of neutral evolution and their study has the potential to reveal intrinsic mutational biases. However, this potential is mitigated by the fact that pseudogenes are quickly purged from bacterial genomes. Here, we assembled a large set of pseudogenes from genomes experiencing reductive evolution as well as functional references for which we could establish reliable phylogenetic relationships. Using this unique dataset, we identified 857 independent insertion and deletion mutations and discover a pervasive bias towards deletions, but not insertions, with sizes multiples of 3 nt. We further show that selective constraints for the preservation of gene frame are unlikely to account for the observed mutational bias and propose that a mechanistic bias in alternative end-joining repair, a recombination-independent double strand break DNA repair mechanism, is responsible for the accumulation of 3n deletions.
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Affiliation(s)
- Bram Danneels
- Department of Biochemistry and Microbiology, Ghent University, Belgium
| | - Marta Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zurich, Switzerland
| | - Aurelien Carlier
- Department of Biochemistry and Microbiology, Ghent University, Belgium
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13
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Pinto-Carbó M, Gademann K, Eberl L, Carlier A. Leaf nodule symbiosis: function and transmission of obligate bacterial endophytes. CURRENT OPINION IN PLANT BIOLOGY 2018; 44:23-31. [PMID: 29452904 DOI: 10.1016/j.pbi.2018.01.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 06/08/2023]
Abstract
Various plant species establish intimate symbioses with bacteria within their aerial organs. The bacteria are contained within nodules or glands often present in distinctive patterns on the leaves, and have been used as taxonomic marker since the early 20th century. These structures are present in very diverse taxa, including dicots (Rubiaceae and Primulaceae) and monocots (Dioscorea). The symbionts colonize the plants throughout their life cycles and contribute bioactive secondary metabolites to the association. In this review, we present recent progress in the understanding of these plant-bacteria symbioses, including the modes of transmission, distribution and roles of the symbionts.
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Affiliation(s)
- Marta Pinto-Carbó
- Department of Microbiology, University of Zurich, CH-8008 Zurich, Switzerland
| | - Karl Gademann
- Department of Chemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Leo Eberl
- Department of Microbiology, University of Zurich, CH-8008 Zurich, Switzerland
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14
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Yang CJ, Hu JM. Bacterial Leaf Nodule Symbiosis in Flowering Plants. Symbiosis 2018. [DOI: 10.5772/intechopen.73078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Crüsemann M, Reher R, Schamari I, Brachmann AO, Ohbayashi T, Kuschak M, Malfacini D, Seidinger A, Pinto‐Carbó M, Richarz R, Reuter T, Kehraus S, Hallab A, Attwood M, Schiöth HB, Mergaert P, Kikuchi Y, Schäberle TF, Kostenis E, Wenzel D, Müller CE, Piel J, Carlier A, Eberl L, König GM. Heterologous Expression, Biosynthetic Studies, and Ecological Function of the Selective Gq‐Signaling Inhibitor FR900359. Angew Chem Int Ed Engl 2018; 57:836-840. [DOI: 10.1002/anie.201707996] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/25/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Max Crüsemann
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Raphael Reher
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Isabella Schamari
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Alexander O. Brachmann
- Institut für MikrobiologieEidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog Weg 4 8093 Zürich Switzerland
| | - Tsubasa Ohbayashi
- Institute for Integrative Biology of the Cell, UMR9198CNRSUniversité Paris‐Sud, CEA Avenue de la Terrasse Gif-sur-Yvette 91198 France
| | - Markus Kuschak
- PharmaCenter BonnPharmazeutisches InstitutPharmazeutische Chemie IUniversität Bonn An der Immenburg 4 53121 Bonn Germany
| | - Davide Malfacini
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Alexander Seidinger
- Institut für Physiologie I, Medizinische FakultätUniversität Bonn, Life&Brain Center Sigmund-Freud-Str. 25 53127 Bonn Germany
| | - Marta Pinto‐Carbó
- Institut für Pflanzen- und MikrobiologieUniversität Zürich Zollikerstr. 107 8008 Zürich Switzerland
| | - René Richarz
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Tatjana Reuter
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Stefan Kehraus
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Asis Hallab
- Pflanzenwissenschaften (IBG-2) Forschungszentrum Jülich Wilhelm-Johnen-Str. 52428 Jülich Germany
| | - Misty Attwood
- Department of Neuroscience, Biomedical CenterUppsala University 751 24 Uppsala Sweden
| | - Helgi B. Schiöth
- Department of Neuroscience, Biomedical CenterUppsala University 751 24 Uppsala Sweden
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR9198CNRSUniversité Paris‐Sud, CEA Avenue de la Terrasse Gif-sur-Yvette 91198 France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute AIST Hokkaido Tsukisamu-higashi 2-17-2-1 Sapporo 062-8517 Japan
| | - Till F. Schäberle
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
- Institut für InsektenbiotechnologieUniversität Gießen Heinrich-Buff-Ring 26–32 35392 Gießen Germany
| | - Evi Kostenis
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
| | - Daniela Wenzel
- Institut für Physiologie I, Medizinische FakultätUniversität Bonn, Life&Brain Center Sigmund-Freud-Str. 25 53127 Bonn Germany
| | - Christa E. Müller
- PharmaCenter BonnPharmazeutisches InstitutPharmazeutische Chemie IUniversität Bonn An der Immenburg 4 53121 Bonn Germany
| | - Jörn Piel
- Institut für MikrobiologieEidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog Weg 4 8093 Zürich Switzerland
| | - Aurélien Carlier
- Department of Biochemistry and MicrobiologyUniversity of Gent K.L. Ledeganckstraat 35, L9 9000 Gent Belgium
| | - Leo Eberl
- Institut für Pflanzen- und MikrobiologieUniversität Zürich Zollikerstr. 107 8008 Zürich Switzerland
| | - Gabriele M. König
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Germany
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16
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Crüsemann M, Reher R, Schamari I, Brachmann AO, Ohbayashi T, Kuschak M, Malfacini D, Seidinger A, Pinto‐Carbó M, Richarz R, Reuter T, Kehraus S, Hallab A, Attwood M, Schiöth HB, Mergaert P, Kikuchi Y, Schäberle TF, Kostenis E, Wenzel D, Müller CE, Piel J, Carlier A, Eberl L, König GM. Heterologe Expression, Biosynthese und ökologische Funktion des selektiven Gq‐Signaltransduktionsinhibitors FR900359. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201707996] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Max Crüsemann
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Raphael Reher
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Isabella Schamari
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Alexander O. Brachmann
- Institut für MikrobiologieEidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Tsubasa Ohbayashi
- Institute for Integrative Biology of the Cell, UMR9198CNRSUniversité Paris‐Sud, CEA Avenue de la Terrasse Gif-sur-Yvette 91198 Frankreich
| | - Markus Kuschak
- PharmaCenter BonnPharmazeutisches InstitutPharmazeutische Chemie IUniversität Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Davide Malfacini
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Alexander Seidinger
- Institut für Physiologie I, Medizinische FakultätUniversität Bonn, Life&Brain Center Sigmund-Freud-Str.25 53127 Bonn Deutschland
| | - Marta Pinto‐Carbó
- Institut für Pflanzen- und MikrobiologieUniversität Zürich Zollikerstrasse 107 8008 Zürich Schweiz
| | - René Richarz
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Tatjana Reuter
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Stefan Kehraus
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Asis Hallab
- Institut für Bio- und GeowissenschaftenPflanzenwissenschaften (IBG-2) Forschungszentrum Jülich Wilhelm-Johnen-Straße 52428 Jülich Deutschland
| | - Misty Attwood
- Department of Neuroscience, Biomedical CenterUppsala University 751 24 Uppsala Schweden
| | - Helgi B. Schiöth
- Department of Neuroscience, Biomedical CenterUppsala University 751 24 Uppsala Schweden
| | - Peter Mergaert
- Institute for Integrative Biology of the Cell, UMR9198CNRSUniversité Paris‐Sud, CEA Avenue de la Terrasse Gif-sur-Yvette 91198 Frankreich
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute AIST Hokkaido Tsukisamu-higashi 2-17-2-1 Sapporo 062-8517 Japan
| | - Till F. Schäberle
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
- Institut für InsektenbiotechnologieUniversität Gießen Heinrich-Buff-Ring 26–32 35392 Gießen Deutschland
| | - Evi Kostenis
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
| | - Daniela Wenzel
- Institut für Physiologie I, Medizinische FakultätUniversität Bonn, Life&Brain Center Sigmund-Freud-Str.25 53127 Bonn Deutschland
| | - Christa E. Müller
- PharmaCenter BonnPharmazeutisches InstitutPharmazeutische Chemie IUniversität Bonn An der Immenburg 4 53121 Bonn Deutschland
| | - Jörn Piel
- Institut für MikrobiologieEidgenössische Technische Hochschule (ETH) Zürich Vladimir-Prelog-Weg 4 8093 Zürich Schweiz
| | - Aurélien Carlier
- Department of Biochemistry and MicrobiologyUniversity of Gent K.L. Ledeganckstraat 35, L9 9000 Gent Belgien
| | - Leo Eberl
- Institut für Pflanzen- und MikrobiologieUniversität Zürich Zollikerstrasse 107 8008 Zürich Schweiz
| | - Gabriele M. König
- Institut für Pharmazeutische BiologieUniversität Bonn Nussallee 6 53115 Bonn Deutschland
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17
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Omasits U, Varadarajan AR, Schmid M, Goetze S, Melidis D, Bourqui M, Nikolayeva O, Québatte M, Patrignani A, Dehio C, Frey JE, Robinson MD, Wollscheid B, Ahrens CH. An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics. Genome Res 2017; 27:2083-2095. [PMID: 29141959 PMCID: PMC5741054 DOI: 10.1101/gr.218255.116] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 10/25/2017] [Indexed: 12/18/2022]
Abstract
Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy toward accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs (a modified six-frame translation considering alternative start codons) in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive Bartonella henselae proteomics data set against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and single amino acid variations (SAAVs) identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin. We release iPtgxDBs for B. henselae, Bradyrhizobium diazoefficiens and Escherichia coli and the software to generate both proteogenomics search databases and integrated annotation files that can be viewed in a genome browser for any prokaryote.
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Affiliation(s)
- Ulrich Omasits
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Adithi R Varadarajan
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland.,Department of Health Sciences and Technology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Michael Schmid
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Sandra Goetze
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Damianos Melidis
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Marc Bourqui
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Olga Nikolayeva
- Institute for Molecular Life Sciences & SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | | | - Andrea Patrignani
- Functional Genomics Center Zurich, ETH & UZH Zurich, CH-8057 Zurich, Switzerland
| | | | - Juerg E Frey
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
| | - Mark D Robinson
- Institute for Molecular Life Sciences & SIB Swiss Institute of Bioinformatics, University of Zurich, CH-8057 Zurich, Switzerland
| | - Bernd Wollscheid
- Department of Health Sciences and Technology, Institute of Molecular Systems Biology, Swiss Federal Institute of Technology Zurich, CH-8093 Zurich, Switzerland
| | - Christian H Ahrens
- Agroscope, Research Group Molecular Diagnostics, Genomics and Bioinformatics & SIB Swiss Institute of Bioinformatics, CH-8820 Wädenswil, Switzerland
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18
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Verstraete B, Janssens S, Rønsted N. Non-nodulated bacterial leaf symbiosis promotes the evolutionary success of its host plants in the coffee family (Rubiaceae). Mol Phylogenet Evol 2017; 113:161-168. [PMID: 28552505 DOI: 10.1016/j.ympev.2017.05.022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 05/23/2017] [Accepted: 05/23/2017] [Indexed: 11/15/2022]
Affiliation(s)
- Brecht Verstraete
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, 1307 Copenhagen, Denmark.
| | | | - Nina Rønsted
- Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83S, 1307 Copenhagen, Denmark.
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19
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Pinto-Carbó M, Sieber S, Dessein S, Wicker T, Verstraete B, Gademann K, Eberl L, Carlier A. Evidence of horizontal gene transfer between obligate leaf nodule symbionts. THE ISME JOURNAL 2016; 10:2092-105. [PMID: 26978165 PMCID: PMC4989318 DOI: 10.1038/ismej.2016.27] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 12/29/2015] [Accepted: 01/12/2016] [Indexed: 01/06/2023]
Abstract
Bacteria of the genus Burkholderia establish an obligate symbiosis with plant species of the Rubiaceae and Primulaceae families. The bacteria, housed within the leaves, are transmitted hereditarily and have not yet been cultured. We have sequenced and compared the genomes of eight bacterial leaf nodule symbionts of the Rubiaceae plant family. All of the genomes exhibit features consistent with genome erosion. Genes potentially involved in the biosynthesis of kirkamide, an insecticidal C7N aminocyclitol, are conserved in most Rubiaceae symbionts. However, some have partially lost the kirkamide pathway due to genome erosion and are unable to synthesize the compound. Kirkamide synthesis is therefore not responsible for the obligate nature of the symbiosis. More importantly, we find evidence of intra-clade horizontal gene transfer (HGT) events affecting genes of the secondary metabolism. This indicates that substantial gene flow can occur at the early stages following host restriction in leaf nodule symbioses. We propose that host-switching events and plasmid conjugative transfers could have promoted these HGTs. This genomic analysis of leaf nodule symbionts gives, for the first time, new insights in the genome evolution of obligate symbionts in their early stages of the association with plants.
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Affiliation(s)
- Marta Pinto-Carbó
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Simon Sieber
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Steven Dessein
- Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
- Botanic Garden, Meise, Belgium
| | - Thomas Wicker
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Brecht Verstraete
- Plant Conservation and Population Biology, KU Leuven, Leuven, Belgium
- Botanic Garden, Meise, Belgium
| | - Karl Gademann
- Department of Chemistry, University of Basel, Basel, Switzerland
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | - Aurelien Carlier
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
- Laboratory of Microbiology, Ghent University, 9000 Belgium, Switzerland
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20
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Carlier A, Fehr L, Pinto-Carbó M, Schäberle T, Reher R, Dessein S, König G, Eberl L. The genome analysis of Candidatus Burkholderia crenata reveals that secondary metabolism may be a key function of the Ardisia crenata leaf nodule symbiosis. Environ Microbiol 2016; 18:2507-22. [PMID: 26663534 DOI: 10.1111/1462-2920.13184] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 12/08/2015] [Indexed: 11/30/2022]
Abstract
A majority of Ardisia species harbour Burkholderia sp. bacteria within specialized leaf nodules. The bacteria are transmitted hereditarily and have not yet been cultured outside of their host. Because the plants cannot develop beyond the seedling stage without their symbionts, the symbiosis is considered obligatory. We sequenced for the first time the genome of Candidatus Burkholderia crenata (Ca. B. crenata), the leaf nodule symbiont of Ardisia crenata. The genome of Ca. B. crenata is the smallest Burkholderia genome to date. It contains a large amount of insertion sequences and pseudogenes and displays features consistent with reductive genome evolution. The genome does not encode functions commonly associated with plant symbioses such as nitrogen fixation and plant hormone metabolism. However, we identified unique genes with a predicted role in secondary metabolism in the genome of Ca. B. crenata. Specifically, we provide evidence that the bacterial symbionts are responsible for the synthesis of compound FR900359, a cyclic depsipeptide with biomedical properties previously isolated from leaves of A. crenata.
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Affiliation(s)
- Aurelien Carlier
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland.,Department of Microbiology, University of Ghent, 9000, Gent, Belgium
| | - Linda Fehr
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
| | - Marta Pinto-Carbó
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
| | - Till Schäberle
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Raphael Reher
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Steven Dessein
- Plant Conservation and Population Biology, KU Leuven, 3001, Leuven, Belgium.,National Botanic Garden of Belgium, 1860, Meise, Belgium
| | - Gabriele König
- Institute for Pharmaceutical Biology, University of Bonn, 53115, Bonn, Germany
| | - Leo Eberl
- Department of Microbiology, University of Zurich, CH-8008, Zurich, Switzerland
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Sieber S, Carlier A, Neuburger M, Grabenweger G, Eberl L, Gademann K. Isolation and Total Synthesis of Kirkamide, an Aminocyclitol from an Obligate Leaf Nodule Symbiont. Angew Chem Int Ed Engl 2015; 54:7968-70. [DOI: 10.1002/anie.201502696] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Indexed: 01/08/2023]
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22
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Sieber S, Carlier A, Neuburger M, Grabenweger G, Eberl L, Gademann K. Isolation and Total Synthesis of Kirkamide, an Aminocyclitol from an Obligate Leaf Nodule Symbiont. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502696] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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A link between arabinose utilization and oxalotrophy in Bradyrhizobium japonicum. Appl Environ Microbiol 2014; 80:2094-101. [PMID: 24463964 DOI: 10.1128/aem.03314-13] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rhizobia have a versatile catabolism that allows them to compete successfully with other microorganisms for nutrients in the soil and in the rhizosphere of their respective host plants. In this study, Bradyrhizobium japonicum USDA 110 was found to be able to utilize oxalate as the sole carbon source. A proteome analysis of cells grown in minimal medium containing arabinose suggested that oxalate oxidation extends the arabinose degradation branch via glycolaldehyde. A mutant of the key pathway genes oxc (for oxalyl-coenzyme A decarboxylase) and frc (for formyl-coenzyme A transferase) was constructed and shown to be (i) impaired in growth on arabinose and (ii) unable to grow on oxalate. Oxalate was detected in roots and, at elevated levels, in root nodules of four different B. japonicum host plants. Mixed-inoculation experiments with wild-type and oxc-frc mutant cells revealed that oxalotrophy might be a beneficial trait of B. japonicum at some stage during legume root nodule colonization.
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