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Intracellular Catalytic Domain of Symbiosis Receptor Kinase Hyperactivates Spontaneous Nodulation in Absence of Rhizobia

Intracellular Catalytic Domain of Symbiosis Receptor Kinase Hyperactivates Spontaneous Nodulation in Absence of Rhizobia | bradyrhizobium diversity | Scoop.it
Symbiosis Receptor Kinase (SYMRK), a member of the Nod factor signaling pathway, is indispensible for both nodule organogenesis and intracellular colonization of symbionts in rhizobia-legume symbiosis. Here, we show that the intracellular kinase domain of a SYMRK (SYMRK-kd) but not its inactive or full-length version leads to hyperactivation of the nodule organogenic program in Medicago truncatula TR25 (symrk knockout mutant) in the absence of rhizobia. Spontaneous nodulation in TR25/SYMRK-kd was 6-fold higher than rhizobia-induced nodulation in TR25/SYMRK roots. The merged clusters of spontaneous nodules indicated that TR25 roots in the presence of SYMRK-kd have overcome the control over both nodule numbers and their spatial position. In the presence of rhizobia, SYMRK-kd could rescue the epidermal infection processes in TR25, but colonization of symbionts in the nodule interior was significantly compromised. In summary, ligand-independent deregulated activation of SYMRK hyperactivates nodule organogenesis in the absence of rhizobia, but its ectodomain is required for proper symbiont colonization.

Via Christophe Jacquet
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Evaluation of the role of the LysM receptor-like kinase, OsNFR5/OsRLK2 for AM symbiosis in rice

In legume-specific rhizobial symbiosis, host plants perceive rhizobial signal molecules, Nod factors, by a couple of LysM receptor like kinases, NFR1/LYK3 and NFR5/NFP, and activate symbiotic responses through the downstream signaling components required also for arbuscular mycorrhizal (AM) symbiosis. Recently, rice NFR1/LYK3 ortholog, OsCERK1, was shown to play crucial roles for AM symbiosis. On the other hand, the roles of NFR5/NFP ortholog in rice have not been elucidated, while it has been shown that NFR5/NFP orthologs, Parasponia PaNFR5 and tomato SlRLK10, engage in AM symbiosis.

OsCERK1 also triggers immune responses in combination with a receptor partner, OsCEBiP, against fungal or bacterial infection, thus regulating opposite responses against symbiotic and pathogenic microbes. However, it has not been elucidated how OsCERK1 switches these opposite functions. Here, we analyzed the function of rice NFR5/NFP ortholog, OsNFR5/OsRLK2, as a possible candidate of the OsCERK1 partner for symbiotic signaling.

Inoculation of AM fungi induced the expression of OsNFR5 in the rice root and the chimeric receptor consisting of the extracellular domain of LjNFR5 and the intracellular domain of OsNFR5 complemented Ljnfr5 mutant for rhizobial symbiosis, indicating that the intracellular kinase domain of OsNFR5 could activate symbiotic signaling in L. japonicus. Although these data suggested the possible involvement of OsNFR5 in AM symbiosis, osnfr5 knockout mutants were colonized by AM fungi similar to the wild-type rice. These observations suggested several possibilities including the presence of functionally redundant genes other than OsNFR5 or involvement of novel ligands, which do not require OsNFR5 for recognition.

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Via Jean-Michel Ané
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Stable fluorescent and enzymatic tagging of Bradyrhizobium diazoefficiens to analyze host-plant infection and colonization

Bradyrhizobium diazoefficiens USDA 100 (formerly named Bradyrhizobium japonicum) can fix dinitrogen when living as endosymbiont in root nodules of soybean and some other legumes. Formation of a functional symbiosis relies on a defined developmental program mediated by controlled gene expression in both symbiotic partners. In contrast to other well studied Rhizobium-legume model systems which have been thoroughly examined by means of genetically tagged strains, analysis of B. diazoefficiens host infection has been impaired due to the lack of suitable tagging systems. Here we describe the construction of B. diazoefficiens strains constitutively expressing single-copy genes for fluorescent proteins (eBFP2, mTurquoise2, GFP+, sYFP2, mCherry, HcRed) and enzymes (GusA, LacZ). For stable inheritance, the constructs were recombined into the chromosome. Effectiveness and versatility of the tagged strains was demonstrated in plant infection assays: (i) The infection process was followed from root hair attachment to colonization of nodule cells with epifluorescent microscopy. (ii) Monitoring mixed infections with two strains producing different fluorescent proteins allowed rapid analysis of nodule occupancy and revealed that the majority of nodules contained clonal populations. (iii) Microscopic analysis of nodules induced by fluorescent strains provided evidence for host-dependent control of B. diazoefficiens bacteroid morphology in nodules of Aeschynomene afraspera and Arachis hypogaea (peanut) as deduced from their altered morphology compared with bacteroids in soybean nodules.

Via Jean-Michel Ané
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Significant nonsymbiotic nitrogen fixation in Patagonian ombrotrophic bogs

Significant nonsymbiotic nitrogen fixation in Patagonian ombrotrophic bogs | bradyrhizobium diversity | Scoop.it
Nitrogen (N) nutrition in pristine peatlands relies on the natural input of inorganic N through atmospheric deposition or biological dinitrogen (N2) fixation. However, N2 fixation and its significance for N cycling, plant productivity, and peat buildup are mostly associated with the presence of Sphagnum mosses. Here, we report high nonsymbiotic N2-fixation rates in two pristine Patagonian bogs with diversified vegetation and natural N deposition. Nonsymbiotic N2 fixation was measured in samples from 0 to 10, 10 to 20, and 40 to 50 cm depth using the 15N2 assay as well as the acetylene reduction assay (ARA). The ARA considerably underestimated N2 fixation and can thus not be recommended for peatland studies. Based on the 15N2 assay, high nonsymbiotic N2-fixation rates of 0.3–1.4 μmol N2 g−1 day−1 were found down to 50 cm under micro-oxic conditions (2 vol.%) in samples from plots covered by Sphagnum magellanicum or by vascular cushion plants, latter characterized by dense and deep aerenchyma roots. Peat N concentrations point to greater potential of nonsymbiotic N2 fixation under cushion plants, likely because of the availability of easily decomposable organic compounds and oxic conditions in the rhizosphere. In the Sphagnum plots, high N2 fixation below 10 cm depth rather reflects the potential during dry periods or low water level when oxygen penetrates the top peat layer and triggers peat mineralization. Natural abundance of the 15N isotope of live Sphagnum (5.6 δ‰) from 0 to 10 cm points to solely N uptake from atmospheric deposition and nonsymbiotic N2 fixation. A mean 15N signature of −0.7 δ‰ of peat from the cushion plant plots indicates additional N supply from N mineralization. Our findings suggest that nonsymbiotic N2 fixation overcomes N deficiency in different vegetation communities and has great significance for N cycling and peat accumulation in pristine peatlands.

Via Jean-Michel Ané
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Adventitious root formation in rice

Adventitious root formation in rice | bradyrhizobium diversity | Scoop.it
The root system is fundamentally important for plants to efficiently obtain nutrients and water. In contrast to the primary root system of plants, roots of monocot cereals consist almost entirely of a complex fibrous system and a mass of adventitious roots (ARs). AR formation is the process of root initiation from the stem base post-embryonically, which is tightly regulated to prevent the loss of valuable plant resources for non-essential root formation. A lack of stable and credible morphological data makes it difficult to study physiological and molecular mechanisms governing AR growth. However, comprehensive understanding of AR development should have important implications for manipulating root architecture, which contributes to both improving crop yield and optimizing agricultural land use.

Via Jean-Michel Ané
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Bifunctional plant receptor, OsCERK1, regulates both chitin-triggered immunity and arbuscular mycorrhizal symbiosis in rice

Bifunctional plant receptor, OsCERK1, regulates both chitin-triggered immunity and arbuscular mycorrhizal symbiosis in rice | bradyrhizobium diversity | Scoop.it
Abstract

Plants are constantly exposed to threats from pathogenic microbes and thus developed innate immune system to protect themselves. On the other hand, many plants also have the ability to establish endosymbiosis with beneficial microbes such as arbuscular mycorrhizal (AM) fungi or rhizobial bacteria, which improves the growth of host plants. How plants evolved the systems managing such opposite plant–microbe interactions is unclear. We here show that KO mutants of OsCERK1, a rice receptor kinase essential for chitin signaling, were impaired not only for chitin-triggered defense responses but also for arbuscular mycorrhizal (AM) symbiosis, indicating the bifunctionality of OsCERK1 in defense and symbiosis. On the other hand, a KO mutant of OsCEBiP, which forms receptor complex with OsCERK1 and is essential for chitin-triggered immunity, established mycorrhizal symbiosis normally. Therefore, OsCERK1 but not chitin-triggered immunity is required for AM symbiosis. Furthermore, experiments with chimeric receptors showed that the kinase domains of OsCERK1 and homologs from non-leguminous, mycorrhizal plants could trigger nodulation signaling in legume–rhizobium interactions as the kinase domain of NFR1, which is essential for triggering the nodulation program in leguminous plants, did. Because leguminous plants are believed to have developed the rhizobial symbiosis on the basis of AM symbiosis, our results suggested that the symbiotic function of ancestral CERK1 in AM symbiosis enabled the molecular evolution to leguminous NFR1 and resulted in the establishment of legume-rhizobia symbiosis. These results also suggested that OsCERK1 and homologs serve as a molecular switch that activates defense or symbiotic responses depending on the infecting microbes.


Via Pierre-Marc Delaux
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How bacteria are like smartphones

How bacteria are like smartphones | bradyrhizobium diversity | Scoop.it
Here is one final post about our recent paper on rhizobium population genomics (1).

Via Peter Young
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an excellent concept....

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Peter Young's curator insight, January 27, 2015 3:23 AM

Here is one final post about our recent paper on rhizobium population genomics (1). For me, it marks an important milestone in my long investigation into the diversity of Rhizobium leguminosarum, which began thirty years ago with the publication of my very first paper on rhizobial diversity (2). Curiously, that paper raised some of the issues that are still being addressed today, as it showed that isolates of symbiovars viciae and trifolii shared a number of distinct chromosomal genotypes. Of course, the tools available at the time allowed only a very blurred picture – it is wonderful to return to the story with the clarity of genome sequencing. If you wonder what I have been doing in the intervening thirty years, you will find a complete list of my publications on Google Scholar (http://scholar.google.co.uk/citations?hl=en&user=ordDMX0AAAAJ&view_op=list_works&sortby=pubdate).   (I recommend that everyone gets a Google Scholar profile – it is such a useful way to keep track of your publications – and those of others.)

Back in 1985, publishing a paper involved massive sheaves of typescript, with glossy photos and hand-inked drawings for the figures. Months after acceptance, your article would arrive in the library in a paper issue of the journal. In the weeks and months after that, you would send out paper reprints in response to requests on postcards and airmail letters (those from India always smelt of curry). Finally, after a year or two, people would start to cite your paper in their own work.

Now, the pace of publication has accelerated, like al aspects of life, as a result of the internet. Our latest paper was accepted a week before Christmas and the final version was published online just two weeks into the new year.   One great thing about online publication is almost instant gratification, because you can immediately see how much interest a publication is generating. The “Info & Metrics” tab on the article’s web page tells me that, since publication on 14 January, our article’s abstract has been viewed 552 times, the full text 1160 times, and the PDF has been downloaded 192 times. Not bad for less than two weeks. I hope all those readers are going to cite our paper!

The article also scores 19 in Altmetrics. This is not something I was really familiar with, but it is based on interest in social media. The article has been blogged once (not including this blog), tweeted by 15 people, and featured on 1 Facebook page. So, thank you to all the rhizobium fans who have tweeted us to stardom! Apparently, an Altmetric of 19 already puts the article in the top 5% of all articles.

Of course, attention on social media does not measure scientific quality, but this did alert me to a couple of interesting web pages. SciGuru (http://www.sciguru.org/newsitem/18225/how-bacteria-are-smartphones) provides short commentaries on interesting recent papers covering all aspects of science. They headlined with “How bacteria are like smartphones”, picking up on an analogy that I used in the press release that I wrote for our university (http://www.york.ac.uk/biology/news-event/news/understandingthepersonalitiesofbacteria/). A Facebook community called Microbiology also featured us on 15 January (https://www.facebook.com/Microbiology.LabRootsPage). One more news item that did not make it into Altmetrics was in an online newspaper called The Speaker (http://thespeaker.co/bacterial-cells-unique-despite-identical-core-genome-due-accessory-packages/).

I don’t usually think of writing a press release when I publish a paper, but in this case I thought the work could be of wider interest, and I was also worried that Open Biology is a relatively new journal, and not yet widely associated with microbiology, so people might miss it. The wider attention came largely through two popular analogies – the idea that bacteria are all indviduals with “personalities”, and that they achieve this by acting like smartphones. Each phone comes out of the factory with standard hardware and operating system (core genome), but gains a unique combination of capabilities through apps (accessory genes) downloaded through the internet (by horizontal gene transfer).

A gimmick, perhaps, but rhizobia do not get enough attention from the rest of the world, so sometimes we rhizobiologists need to wave our arms a bit.

 

Kumar, N., Lad, G., Giuntini, E., Kaye, M. E., Udomwong, P., Shamsani, N. J., Young, J. P. W. & Bailly, X. (2015). Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum. Open Biology, 5(1), 140133.

http://rsob.royalsocietypublishing.org/content/5/1/140133

 

Young, J. P. W. (1985). Rhizobium population genetics: enzyme polymorphism in isolates from peas, clover, beans and lucerne grown at the same site. Journal of General Microbiology, 131, 2399-2408.

http://mic.sgmjournals.org/content/131/9/2399.short

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Characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in Qinghai-Tibet plateau and... Arch Microbiol 2007

Characterization of symbiotic and endophytic bacteria isolated from root nodules of herbaceous legumes grown in Qinghai-Tibet plateau and... Arch Microbiol 2007 | bradyrhizobium diversity | Scoop.it

Abstract

Qinghai–Tibet plateau is the highest place in the world and the environment in that plateau is hard for animals and plants, with low temperature, low concentration of oxygen and high solar radiation. In this study, 61 root nodule isolates from Vicia, Oxytropis, Medicago, Melilotus and Onobrychisspecies grown in Qinghai–Tibet plateau and in loess plateau were comparatively characterized. Based upon the results of numerical taxonomy, ARDRA, AFLP, DNA–DNA hybridization and 16S rDNA sequencing, the isolates were classified as Rhizobium leguminosarum, Sinorhizobium meliloti,Sinorhizobium fredii, Mesorhizobium sp., Phyllobacterium sp., Stenotrophomonas sp. and two non-symbiotic groups related to Agrobacterium and Enterobacteriaceae. The strains isolated from Qinghai–Tibet plateau and from the loess plateau were mixed in these species or groups. Oxytropisspp. and Medicago archiducis-nicolai grown in Qinghai–Tibet plateau were recorded as new hosts for R. leguminosarum, as well as Oxytropis glabra and Medicago lupulina for S. fredii. In addition, strains resistant to high alkaline (pH 11) and high concentration of NaCl (3–5%, w/v) were found in each of the rhizobial species. This was the first systematic study of rhizobia isolated from Qinghai–Tibet plateau


Via Chang Fu Tian
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Transcriptomic analysis of Sinorhizobium meliloti and Medicago truncatula symbiosis using nitrogen fixation deficient nodules

The bacterium Sinorhizobium meliloti interacts symbiotically with legume plant hosts such as Medicago truncatula to form nitrogen-fixing root nodules. During symbiosis, plant and bacterial cells differentiate in a coordinated manner, resulting in specialized plant cells that contain nitrogen-fixing bacteroids. Both plant and bacterial genes are required at each developmental stage of symbiosis. We analyzed gene expression in nodules formed by wild type bacteria on six plant mutants with defects in nitrogen fixation (dnf). We observed differential expression of 482 S. meliloti genes with functions in cell envelope homeostasis, cell division, stress response, energy metabolism and nitrogen fixation. We simultaneously analyzed gene expression in M. truncatula and observed differential regulation of host processes that may trigger bacteroid differentiation and control bacterial infection. Our analyses of developmentally arrested plant mutants indicate that plants use distinct means to control bacterial infection during early and late symbiotic stages.

Via Jean-Michel Ané
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Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis

Proteomic analysis of free-living Bradyrhizobium diazoefficiens: highlighting potential determinants of a successful symbiosis | bradyrhizobium diversity | Scoop.it

Strain CPAC 7 (=SEMIA 5080) was recently reclassified into the new species Bradyrhizobium diazoefficiens; due to its outstanding efficiency in fixing nitrogen, it has been used in commercial inoculants for application to crops of soybean [Glycine max (L.) Merr.] in Brazil and other South American countries. Although the efficiency of B. diazoefficiens inoculant strains is well recognized, few data on their protein expression are available.

Results

We provided a two-dimensional proteomic reference map of CPAC 7 obtained under free-living conditions, with the successful identification of 115 spots, representing 95 different proteins. The results highlighted the expression of molecular determinants potentially related to symbiosis establishment (e.g. inositol monophosphatase, IMPase), fixation of atmospheric nitrogen (N2) (e.g. NifH) and defenses against stresses (e.g. chaperones). By using bioinformatic tools, it was possible to attribute probable functions to ten hypothetical proteins. For another ten proteins classified as "NO related COG" group, we analyzed by RT-qPCR the relative expression of their coding-genes in response to the nodulation-gene inducer genistein. Six of these genes were up-regulated, including blr0227, which may be related to polyhydroxybutyrate (PHB) biosynthesis and competitiveness for nodulation.

Conclusions

The proteomic map contributed to the identification of several proteins of B. diaozoefficiens under free-living conditions and our approach--combining bioinformatics and gene-expression assays--resulted in new information about unknown genes that might play important roles in the establishment of the symbiosis with soybean.


Via Christophe Jacquet, IvanOresnik, Yuanchun Wang
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David Kuykendall's curator insight, August 24, 2014 7:57 AM

This new species includes strain USDA110, an agriculturally superb soybean inoculant strain. The study seems to suggest new pathways of efficient symbiotic nitrogen fixation heretofor uncharacterized. I like it, I like it very much.

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Peribacteroid space acidification: a marker of mature bacteroid functioning in Medicago truncatula nodules

Peribacteroid space acidification: a marker of mature bacteroid functioning in Medicago truncatula nodules | bradyrhizobium diversity | Scoop.it

Legumes form a symbiotic interaction with Rhizobiaceae bacteria, which differentiate into nitrogen-fixing bacteroids within nodules. Here, we investigated in vivo the pH of the peribacteroid space (PBS) surrounding the bacteroid and pH variation throughout symbiosis. In vivoconfocal microscopy investigations, using acidotropic probes, demonstrated the acidic state of the PBS. In planta analysis of nodule senescence induced by distinct biological processes drastically increased PBS pH in the N2-fixing zone (zone III). Therefore, the PBS acidification observed in mature bacteroids can be considered as a marker of bacteroid N2 fixation. Using a pH-sensitive ratiometric probe, PBS pH was measured in vivo during the whole symbiotic process. We showed a progressive acidification of the PBS from the bacteroid release up to the onset of N2 fixation. Genetic and pharmacological approaches were conducted and led to disruption of the PBS acidification. Altogether, our findings shed light on the role of PBS pH of mature bacteroids in nodule functioning, providing new tools to monitor in vivo bacteroid physiology.

 

OLIVIER PIERRE, GILBERT ENGLER, JULIE HOPKINS, FRÉDÉRIC BRAU, ERIC BONCOMPAGNI, DIDIER HÉROUART (2013). Plant Cell and Environment 36: 2059-2070.

 


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Exploring the Intrinsic Limits of Nitrogenase Transfer from Bacteria to Eukaryotes.

Biological nitrogen fixation is widespread among the Eubacteria and Archae domains but completely absent in eukaryotes. The lack of lateral transfer of nitrogen-fixation genes from prokaryotes to eukaryotes has been partially attributed to the physiological requirements necessary for the function of the nitrogenase complex. However, symbiotic bacterial nitrogenase activity is protected by the nodule, a plant structure whose organogenesis can be trigged in the absence of bacteria. To explore the intrinsic potentiality of this plant organ, we generated rhizobium-independent nodules in alfalfa by overexpressing the MsDMI3 kinase lacking the autoinhibitory domain. These transgenic nodules showed similar levels of leghemoglobin, free oxygen, ATP, and NADPH to those of efficient Sinorhizobium meliloti B399-infected nodules, suggesting that the rhizobium-independent nodules can provide an optimal microenvironment for nitrogenase activity. Finally, we discuss the intrinsic evolutionary constraints on transfer of nitrogen-fixation genes between bacteria and eukaryotes.

 Soto G, Fox AR, Ayub ND. (2013).  J Mol Evol. Aug 11. [Epub ahead of print]


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Jean-Michel Ané's curator insight, August 15, 2013 11:51 AM

Alfalfa (Medicago sativa) devellops spontaneous (rhizobium-independent) nodules naturally.... No need to express the DMI3 kinase domain to get spontaneous nodules in alfalfa.

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Versatile Vectors for Efficient Mutagenesis of Bradyrhizobium diazoefficiens and Other Alphaproteobacteria. - PubMed - NCBI

Versatile Vectors for Efficient Mutagenesis of Bradyrhizobium diazoefficiens and Other Alphaproteobacteria. - PubMed - NCBI | bradyrhizobium diversity | Scoop.it
Appl Environ Microbiol. 2016 Apr 18;82(9):2791-9. doi: 10.1128/AEM.04085-15. Print 2016 May. Research Support, Non-U.S. Gov't
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Segregation of nod-containing and nod-deficient bradyrhizobia as endosymbionts of Arachis hypogaea and as endophytes of Oryza sativa in intercropped fields of Bengal Basin, India

Bradyrhizobial invasion in dalbergoid legumes like Arachis hypogaea and endophytic bacterial invasions in non-legumes like Oryza sativa occur through epidermal cracks. Here we show that there is no overlap between the bradyrhizobial consortia that endosymbiotically and endophytically colonise these plants. To minimise contrast due to phylogeographic isolation, strains were collected from Arachis/Oryza intercropped fields and a total of 17 bradyrhizobia from Arachis (WBAH) and 13 from Oryza (WBOS) were investigated. 16SrRNA and concatenated dnaK-glnII-recA phylogeny clustered the nodABC-positive WBAH and nodABC-deficient WBOS strains in two distinct clades. The in-field segregation is reproducible under controlled conditions which limits the factors that influence their competitive exclusion. While WBAH renodulated Arachis successfully, WBOS nodulated in an inefficient manner. Thus Arachis, like other Aeschynomene legumes support nod-independent symbiosis that was ineffectual in natural fields. In Oryza, WBOS recolonised endophytically and promoted its growth. WBAH however caused severe chlorosis that was completely overcome when coinfected with WBOS. This explains the exclusive recovery of WBOS in Oryza in natural fields and suggests Nod-factors to have a role in counterselection of WBAH. Finally, canonical soxY1 and thiosulphate oxidation could only be detected in WBOS indicating loss of metabolic traits in WBAH with adaptation of symbiotic lifestyle. This article is protected by copyright. All rights reserved.

Via Jean-Michel Ané
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Survival and Competitiveness of Bradyrhizobium ...

Survival and Competitiveness of Bradyrhizobium ... | bradyrhizobium diversity | Scoop.it
It was previously demonstrated that there are no indigenous strains of Bradyrhizobium japonicum forming nitrogen-fixing root nodule symbioses with soybean plants in arable field soils in Poland.
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An Autophosphorylation Site Database for Leucine-Rich Repeat Receptor-Like Kinases in Arabidopsis thaliana

An Autophosphorylation Site Database for Leucine-Rich Repeat Receptor-Like Kinases in Arabidopsis thaliana | bradyrhizobium diversity | Scoop.it
Leucine-rich repeat receptor-like kinases (LRR RLKs) form a large family of plant signaling proteins consisting of an extracellular domain connected by a single-pass transmembrane sequence to a cytoplasmic kinase domain. Autophosphorylation on specific Ser and/or Thr residues in the cytoplasmic domain is often critical for the activation of several LRR RLK family members with proven functional roles in plant growth regulation, morphogenesis, disease resistance, and stress responses. While identification and functional characterization of in vivo phosphorylation sites is ultimately required for full understanding of LRR RLK biology and function, bacterial expression of recombinant LRR RLK cytoplasmic catalytic domains for identification of in vitro autophosphorylation sites provides a useful resource for further targeted identification and functional analysis of in vivo sites. In this study we employed high-throughput cloning and a variety of mass spectrometry approaches to generate an autophosphorylation site database representative of more than 30% of the approximately 223 LRR RLKs in Arabidopsis thaliana. His-tagged constructs of complete cytoplasmic domains were used to identify a total of 591 phosphorylation events across 73 LRR RLKs, with 496 sites uniquely assigned to specific Ser (268 sites) or Thr (228 sites) residues in 68 LRR RLKs. Multiple autophosphorylation sites per LRR RLK were the norm, with an average of seven sites per cytoplasmic domain, while some proteins showed more than 20 unique autophosphorylation sites. The database was used to analyze trends in the localization of phosphorylation sites across cytoplasmic kinase subdomains, and to derive a statistically significant sequence motif for phosphoSer autophosphorylation.

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Jean-Michel Ané's curator insight, May 21, 2015 1:02 PM

That should be super useful but... where is this database??

weiweiwei's curator insight, December 25, 2015 10:31 PM

11

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Genomes of mycorrhizal fungi

Within the framework of the JGI Mycorrhizal Genomics Initiative (MGI) project, we are sequencing a phylogenetically and ecologically diverse suite of mycorrhizal fungi (Basidiomycota and Ascomycota), which include the major clades of symbiotic species associating with trees and woody shrubs. Analyses of these genomes will provide new insights into the diversity of mechanisms for the mycorrhizal symbioses, including ericoid-, orchidoid- and ectomycorrhizal associations. A large collaborative effort led by PI of these project, Francis Martin (INRA), aims for master publication(s) of the MGI data analyses. Researchers who wish to publish analyses using data from unpublished MGI genomes are respectfully required to contact the PIs and JGI to avoid potential conflicts on data use and coordinate other publications with the MGI master paper(s).

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The receptor kinase CERK1 has dual functions in symbiosis and immunity signalling - Zhang - 2014 - The Plant Journal - Wiley Online Library

The receptor kinase CERK1 has dual functions in symbiosis and immunity signalling - Zhang - 2014 - The Plant Journal - Wiley Online Library | bradyrhizobium diversity | Scoop.it
Summary

The establishment of symbiotic interactions between mycorrhizal fungi, rhizobial bacteria and their legume hosts involves a common symbiosis signalling pathway. This signalling pathway is activated by Nod factors produced by rhizobia and these are recognised by the Nod factor receptors NFR1/LYK3 and NFR5/NFP. Mycorrhizal fungi produce lipochitooligosaccharides (LCOs) similar to Nod factors, as well as short-chain chitin oligomers (CO4/5), implying commonalities in signalling during mycorrhizal and rhizobial associations. Here we show that NFR1/LYK3, but not NFR5/NFP, is required for the establishment of the mycorrhizal interaction in legumes. NFR1/LYK3 is necessary for the recognition of mycorrhizal fungi and the activation of the symbiosis signalling pathway leading to induction of calcium oscillations and gene expression. Chitin oligosaccharides also act as microbe associated molecular patterns that promote plant immunity via similar LysM receptor-like kinases. CERK1 in rice has the highest homology to NFR1 and we show that this gene is also necessary for the establishment of the mycorrhizal interaction as well as for resistance to the rice blast fungus. Our results demonstrate thatNFR1/LYK3/OsCERK1 represents a common receptor for chitooligosaccharide-based signals produced by mycorrhizal fungi, rhizobial bacteria (in legumes) and fungal pathogens. It would appear that mycorrhizal recognition has been conserved in multiple receptors across plant species, but additional diversification in certain plant species has defined other signals that this class of receptors can perceive.


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Does SUNN-SYMRK Crosstalk occur in Medicago truncatula for regulating nodule organogenesis? - PubMed - NCBI

Does SUNN-SYMRK Crosstalk occur in Medicago truncatula for regulating nodule organogenesis? - PubMed - NCBI | bradyrhizobium diversity | Scoop.it
Plant Signal Behav. 2015 Apr 20:0. [Epub ahead of print]
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Intervention of Phytohormone Pathways by Pathogen Effectors

Intervention of Phytohormone Pathways by Pathogen Effectors | bradyrhizobium diversity | Scoop.it

The constant struggle between plants and microbes has driven the evolution of multiple defense strategies in the host as well as offense strategies in the pathogen. To defend themselves from pathogen attack, plants often rely on elaborate signaling networks regulated by phytohormones. In turn, pathogens have adopted innovative strategies to manipulate phytohormone-regulated defenses. Tactics frequently employed by plant pathogens involve hijacking, evading, or disrupting hormone signaling pathways and/or crosstalk. As reviewed here, this is achieved mechanistically via pathogen-derived molecules known as effectors, which target phytohormone receptors, transcriptional activators and repressors, and other components of phytohormone signaling in the host plant. Herbivores and sap-sucking insects employ obligate pathogens such as viruses, phytoplasma, or symbiotic bacteria to intervene with phytohormone-regulated defenses. Overall, an improved understanding of phytohormone intervention strategies employed by pests and pathogens during their interactions with plants will ultimately lead to the development of new crop protection strategies.


Via Suayib Üstün, Yuanchun Wang
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Rescooped by Sohini Guha from t3ss effectors
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BMC Research Notes | Full text | New players in the same old game: a system level in silico study to predict type III secretion system and effector proteins in bacterial genomes reveals common them...

AbstractBackground Type III secretion system (T3SS) plays an important role in virulence or symbiosis of many pathogenic or symbiotic bacteria [CHM 2:291–294, 2007; Physiology (Bethesda) 20:326–339, 2005]. T3SS acts like a tunnel between a bacterium and its host through which the bacterium injects ‘effector’ proteins into the latter [Nature 444:567–573, 2006; COSB 18:258–266, 2008]. The effectors spatially and temporally modify the host signalling pathways [FEMS Microbiol Rev 35:1100–1125, 2011; Cell Host Microbe5:571–579, 2009]. In spite its crucial role in host-pathogen interaction, the study of T3SS and the associated effectors has been limited to a few bacteria [Cell Microbiol 13:1858–1869, 2011; Nat Rev Microbiol 6:11–16, 2008; Mol Microbiol 80:1420–1438, 2011]. Before one set out to perform systematic experimental studies on an unknown set of bacteria it would be beneficial to identify the potential candidates by developing an in silico screening algorithm. A system level study would also be advantageous over traditional laboratory methods to extract an overriding theme for host-pathogen interaction, if any, from the vast resources of data generated by sequencing multiple bacterial genomes. Results We have developed an in silico protocol in which the most conserved set of T3SS proteins was used as the query against the entire bacterial database with increasingly stringent search parameters. It enabled us to identify several uncharacterized T3SS positive bacteria. We adopted a similar strategy to predict the presence of the already known effectors in the newly identified T3SS positive bacteria. The huge resources of biochemical data [FEMS Microbiol Rev 35:1100–1125, 2011; Cell Host Microbe 5:571–579, 2009; BMC Bioinformatics 7(11):S4, 2010] on the T3SS effectors enabled us to search for the common theme in T3SS mediated pathogenesis. We identified few cellular signalling networks in the host, which are manipulated by most of the T3SS containing pathogens. We went on to look for correlation, if any, between the biological quirks of a particular class of bacteria with the effectors they harbour. We could pin point few effectors, which were enriched in certain classes of bacteria. Conclusion The current study would open up new avenues to explore many uncharacterized T3SS positive bacteria. The experimental validation of the predictions from this study will unravel a generalized mechanism for T3SS positive bacterial infection into host cell. Keywords: T3SS; Effector; Intracellular pathogen; Cytoskeletal structure


Via Yuanchun Wang
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Rescooped by Sohini Guha from Plant-Microbe Symbiosis
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Symbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia

Extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (ISs) and are termed highly reiterated sequence–possessing (HRS) strains. We analyzed the genome organization of HRS strains with the focus on IS distribution and symbiosis island structure. Using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07–0.4 Mb) in the HRS strains (NK5, NK6, USDA135, 2281, USDA123, and T2), whereas no plasmids were detected in the non-HRS strain USDA110. The chromosomes of the six HRS strains (9.7–10.7 Mb) were larger than that of USDA110 (9.1 Mb). Using MiSeq sequences of 6 HRS and 17 non-HRS strains mapped to the USDA110 genome, we found that the copy numbers of ISRj1, ISRj2, ISFK1, IS1632, ISB27, ISBj8, and IS1631 were markedly higher in HRS strains. Whole-genome sequencing showed that the HRS strain NK6 had four small plasmids (136–212 kb) and a large chromosome (9780 kb). Strong co-linearity was found between 7.4-Mb core regions of NK6 and USDA110 chromosomes. USDA110 symbiosis islands mainly corresponded to five small regions (S1–S5) within two variable regions, V1 (0.8 Mb) and V2 (1.6 Mb), of the NK6 chromosome. USDA110 nif gene cluster (nifDKENXSBZHQW/fixBCX) was split into two regions, S2 and S3, where ISRj1-mediated rearrangement occurred between nifS and nifB. ISs were also scattered in NK6 core regions, and ISRj1 insertion often disrupted some genes important for survival and environmental responses. These results suggest that HRS strains of soybean bradyrhizobia were subjected to IS-mediated symbiosis island shuffling and core genome degradation.

Via Jean-Michel Ané
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Rescooped by Sohini Guha from Rhizobium Research
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Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system

Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system | bradyrhizobium diversity | Scoop.it

Root–nodule symbiosis between leguminous plants and nitrogen-fixing bacteria (rhizobia) involves molecular communication between the two partners. Key components for the establishment of symbiosis are rhizobium-derived lipochitooligosaccharides (Nod factors; NFs) and their leguminous receptors (NFRs) that initiate nodule development and bacterial entry. Here we demonstrate that the soybean microsymbiontBradyrhizobium elkanii uses the type III secretion system (T3SS), which is known for its delivery of virulence factors by pathogenic bacteria, to promote symbiosis. Intriguingly, wild-type B. elkanii, but not the T3SS-deficient mutant, was able to form nitrogen-fixing nodules on soybean nfr mutant En1282. Furthermore, even the NF-deficient B. elkanii mutant induced nodules unless T3SS genes were mutated. Transcriptional analysis revealed that expression of the soybean nodulation-specific genes ENOD40 and NIN was increased in the roots of En1282 inoculated with B. elkanii but not with its T3SS mutant, suggesting that T3SS activates host nodulation signaling by bypassing NF recognition. Root-hair curling and infection threads were not observed in the roots of En1282 inoculated with B. elkanii, indicating that T3SS is involved in crack entry or intercellular infection. These findings suggest that B. elkanii has adopted a pathogenic system for activating host symbiosis signaling to promote its infection.


Via Jean-Michel Ané, IvanOresnik
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Steve Marek's curator insight, October 2, 2013 11:44 AM

Changing the paradigm..."nod factors? we don't need no stinking nod factors'

Rescooped by Sohini Guha from Rhizobium Research
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Host-specific Nod-factors associated with Medicago truncatula nodule infection differentially induce calcium influx and calcium spiking in root hairs.

Host-specific Nod-factors associated with Medicago truncatula nodule infection differentially induce calcium influx and calcium spiking in root hairs. | bradyrhizobium diversity | Scoop.it

Rhizobial nodulation (Nod) factors activate both nodule morphogenesis and infection thread development during legume nodulation. Nod factors induce two different calcium responses: intra-nuclear calcium oscillations and a calcium influx at the root hair tip. Calcium oscillations activate nodule development; we wanted to test if the calcium influx is associated with infection. Sinorhizobium meliloti nodL and nodF mutations additively reduce infection of Medicago truncatula. Nod-factors made by the nodL mutant lack an acetyl group; mutation of nodF causes the nitrogen (N)-linked C16:2 acyl chain to be replaced by C18:1. We tested whether these Nod-factors differentially induced calcium influx and calcium spiking. The absence of the NodL-determined acetyl group greatly reduced the induction of calcium influx without affecting calcium spiking. The calcium influx was even further reduced if the N-linked C16:2 acyl group was replaced by C18:1. These additive effects on calcium influx correlate with the additive effects of mutations in nodF and nodL on legume infection. Infection thread development is inhibited by ethylene, which also inhibited Nod-factor-induced calcium influx. We conclude that Nod-factor perception differentially activates the two developmental pathways required for nodulation and that activation of the pathway involving the calcium influx is important for efficient infection.

 

Morieri G, Martinez EA, Jarynowski A, Driguez H, Morris R, Oldroyd GE, Downie JA. (2013).  New Phytol. Sep 10. doi: 10.1111/nph.12475. [Epub ahead of print]


Via IvanOresnik
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