scholarly journals A Link between Arabinose Utilization and Oxalotrophy in Bradyrhizobium japonicum

2014 ◽  
Vol 80 (7) ◽  
pp. 2094-2101 ◽  
Author(s):  
Marion Koch ◽  
Nathanaël Delmotte ◽  
Christian H. Ahrens ◽  
Ulrich Omasits ◽  
Kathrin Schneider ◽  
...  
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Host Plants ◽  
Root Nodule ◽  
Coenzyme A ◽  
Root Nodules ◽  
Proteome Analysis ◽  
Wild Type ◽  
Content Type ◽  
Mutant Cells ◽  
Respective Host

ABSTRACTRhizobia 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 japonicumUSDA 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 genesoxc(for oxalyl-coenzyme A decarboxylase) andfrc(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 differentB. japonicumhost plants. Mixed-inoculation experiments with wild-type andoxc-frcmutant cells revealed that oxalotrophy might be a beneficial trait ofB. japonicumat some stage during legume root nodule colonization.

scholarly journals Phenylacetyl Coenzyme A, Not Phenylacetic Acid, Attenuates CepIR-Regulated Virulence in Burkholderia cenocepacia

2019 ◽  
Vol 85 (24) ◽  
Author(s):  
Tasia Joy Lightly ◽  
Kara L. Frejuk ◽  
Marie-Christine Groleau ◽  
Laurent R. Chiarelli ◽  
Cor Ras ◽  
...  
Keyword(s):  
Quorum Sensing ◽  
Phenylacetic Acid ◽  
Coenzyme A ◽  
Opportunistic Pathogen ◽  
Burkholderia Cenocepacia ◽  
Signal Molecules ◽  
Wild Type ◽  
Content Type ◽  
Opportunistic Bacteria ◽  
Virulent Phenotype

ABSTRACT During phenylalanine catabolism, phenylacetic acid (PAA) is converted to phenylacetyl coenzyme A (PAA-CoA) by a ligase, PaaK, and then PAA-CoA is epoxidized by a multicomponent monooxygenase, PaaABCDE, before further degradation through the tricarboxylic acid (TCA) cycle. In the opportunistic pathogen Burkholderia cenocepacia, loss of paaABCDE attenuates virulence factor expression, which is under the control of the LuxIR-like quorum sensing (QS) system, CepIR. To further investigate the link between CepIR-regulated virulence and PAA catabolism, we created knockout mutants of the first step of the pathway (PAA-CoA synthesis by PaaK) and characterized them in comparison to a paaABCDE mutant using liquid chromatography-tandem mass spectrometry (LC-MS/MS) and virulence assays. We found that while loss of PaaABCDE decreased virulence, deletion of the paaK genes resulted in a more virulent phenotype than that of the wild-type strain. Deletion of either paaK or paaABCDE led to higher levels of released PAA but no differences in levels of internal accumulation compared to the wild-type level. While we found no evidence of direct cepIR downregulation by PAA-CoA or PAA, a low-virulence cepR mutant reverted to a virulent phenotype upon removal of the paaK genes. On the other hand, removal of paaABCDE in the cepR mutant did not impact its attenuated phenotype. Together, our results suggest an indirect role for PAA-CoA in suppressing B. cenocepacia CepIR-activated virulence. IMPORTANCE The opportunistic pathogen Burkholderia cenocepacia uses a chemical signal process called quorum sensing (QS) to produce virulence factors. In B. cenocepacia, QS relies on the presence of the transcriptional regulator CepR which, upon binding QS signal molecules, activates virulence. In this work, we found that even in the absence of CepR, B. cenocepacia can elicit a pathogenic response if phenylacetyl-CoA, an intermediate of the phenylacetic acid degradation pathway, is not produced. Instead, accumulation of phenylacetyl-CoA appears to attenuate pathogenicity. Therefore, we have discovered that it is possible to trigger virulence in the absence of CepR, challenging the classical view of activation of virulence by this QS mechanism. Our work provides new insight into the relationship between metabolism and virulence in opportunistic bacteria. We propose that in the event that QS signaling molecules cannot accumulate to trigger a pathogenic response, a metabolic signal can still activate virulence in B. cenocepacia.

scholarly journals FrankiaDiversity in Host Plant Root Nodules Is Independent of Abundance or Relative Diversity ofFrankiaPopulations in Corresponding Rhizosphere Soils

2017 ◽  
Vol 84 (5) ◽  
Author(s):  
Seifeddine Ben Tekaya ◽  
Trina Guerra ◽  
David Rodriguez ◽  
Jeffrey O. Dawson ◽  
Dittmar Hahn
Keyword(s):  
Host Plant ◽  
Root Nodule ◽  
Root Nodules ◽  
Actinorhizal Plants ◽  
Nodule Formation ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Rhizosphere Soils ◽  
Root Nodule Formation ◽  
Host Infection

ABSTRACTActinorhizal plants form nitrogen-fixing root nodules in symbiosis with soil-dwelling actinobacteria within the genusFrankia, and specificFrankiataxonomic clusters nodulate plants in corresponding host infection groups. In same-soil microcosms, we observed that some host species were nodulated (Alnus glutinosa,Alnus cordata,Shepherdia argentea,Casuarina equisetifolia) while others were not (Alnus viridis,Hippophaë rhamnoides). Nodule populations were represented by eight different sequences ofnifHgene fragments. Two of these sequences characterized frankiae inS. argenteanodules, and three others characterized frankiae inA. glutinosanodules. Frankiae inA. cordatanodules were represented by five sequences, one of which was also found in nodules fromA. glutinosaandC. equisetifolia, while another was detected in nodules fromA. glutinosa. Quantitative PCR assays showed that vegetation generally increased the abundance of frankiae in soil, independently of the target gene (i.e.,nifHor the 23S rRNA gene). Targeted Illumina sequencing ofFrankia-specificnifHgene fragments detected 24 unique sequences from rhizosphere soils, 4 of which were also found in nodules, while the remaining 4 sequences in nodules were not found in soils. Seven of the 24 sequences from soils represented >90% of the reads obtained in most samples; the 2 most abundant sequences from soils were not found in root nodules, and only 2 of the sequences from soils were detected in nodules. These results demonstrate large differences between detectableFrankiapopulations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specificFrankiapopulations in soils.IMPORTANCEThe nitrogen-fixing actinobacteriumFrankiaforms root nodules on actinorhizal plants, with members of specificFrankiataxonomic clusters nodulating plants in corresponding host infection groups. We assessedFrankiadiversity in root nodules of different host plant species, and we related specific populations to the abundance and relative distribution of indigenous frankiae in rhizosphere soils. Large differences were observed between detectableFrankiapopulations in soil and those in root nodules, suggesting that root nodule formation is not a function of the abundance or relative diversity of specificFrankiapopulations in soils but rather results from plants potentially selecting frankiae from the soil for root nodule formation. These data also highlight the necessity of using a combination of different assessment tools so as to adequately address methodological constraints that could produce contradictory data sets.

scholarly journals Rhizobium etli Mutant Modulates Carbon and Nitrogen Metabolism in Phaseolus vulgaris Nodules

2002 ◽  
Vol 15 (7) ◽  
pp. 728-733 ◽  
Author(s):  
Sonia Silvente ◽  
Lourdes Blanco ◽  
Alberto Camas ◽  
José-Luis Ortega ◽  
Mario Ramírez ◽  
...  
Keyword(s):  
Root Nodule ◽  
Root Nodules ◽  
Glutamate Synthase ◽  
Rhizobium Etli ◽  
Wild Type ◽  
Respiratory Capacity ◽  
Carbon And Nitrogen ◽  
N Assimilation ◽  
Mutant Strains ◽  
Carbon And Nitrogen Metabolism

The aim of this study was to evaluate the biochemical events in root nodules which lead to increased yield when bean is inoculated with a Rhizobium etli mutant (CFN037) having increased respiratory capacity. CFN037-inoculated plants had 22% more nitrogen (N) than did wild-type (CE3)-inoculated plants. Root nodule enzymes involved in nodule carbon and nitrogen assimilation as well as in ureides and amides synthesis were assessed in plants inoculated with CFN037 and the CE3. Our results show that the xylem ureides content was lower while that of amino acids was higher in CFN037- compared with CE3-inoculated plants. Supporting these results, enzymes involved in ureide synthesis were reduced while activity of aspartate aminotransferase, glutamate synthase, sucrose synthase, and glucose-6-P dehydrogenase were increased in CFN037- induced nodules. Glutamate synthase and phosphoenolpyruvate carboxylase transcripts were detected early in the development of nodules induced by CFN037 compared with CE3. However, plants inoculated with strain CE3-vhb, which express the Vitreoscilla sp. hemoglobin and also displays increased respiratory capacity, did not have altered ureide transport in N2-fixing plants. The data suggest that inoculation with special selected mutant strains of R. etli can modulate nodule N assimilation and N transport compounds.

scholarly journals The Influence of the Host Plant Is the Major Ecological Determinant of the Presence of Nitrogen-Fixing Root Nodule Symbiont Cluster II Frankia Species in Soil

2016 ◽  
Vol 83 (1) ◽  
Author(s):  
Kai Battenberg ◽  
Jannah A. Wren ◽  
Janell Hillman ◽  
Joseph Edwards ◽  
Liujing Huang ◽  
...  
Keyword(s):  
Host Plant ◽  
Host Plants ◽  
Root Nodule ◽  
Rhizosphere Soil ◽  
Broad Host Range ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Microbiome Analysis ◽  
Α Diversity ◽  
Significant Difference

ABSTRACT The actinobacterial genus Frankia establishes nitrogen-fixing root nodule symbioses with specific hosts within the nitrogen-fixing plant clade. Of four genetically distinct subgroups of Frankia, cluster I, II, and III strains are capable of forming effective nitrogen-fixing symbiotic associations, while cluster IV strains generally do not. Cluster II Frankia strains have rarely been detected in soil devoid of host plants, unlike cluster I or III strains, suggesting a stronger association with their host. To investigate the degree of host influence, we characterized the cluster II Frankia strain distribution in rhizosphere soil in three locations in northern California. The presence/absence of cluster II Frankia strains at a given site correlated significantly with the presence/absence of host plants on the site, as determined by glutamine synthetase (glnA) gene sequence analysis, and by microbiome analysis (16S rRNA gene) of a subset of host/nonhost rhizosphere soils. However, the distribution of cluster II Frankia strains was not significantly affected by other potential determinants such as host-plant species, geographical location, climate, soil pH, or soil type. Rhizosphere soil microbiome analysis showed that cluster II Frankia strains occupied only a minute fraction of the microbiome even in the host-plant-present site and further revealed no statistically significant difference in the α-diversity or in the microbiome composition between the host-plant-present or -absent sites. Taken together, these data suggest that host plants provide a factor that is specific for cluster II Frankia strains, not a general growth-promoting factor. Further, the factor accumulates or is transported at the site level, i.e., beyond the host rhizosphere. IMPORTANCE Biological nitrogen fixation is a bacterial process that accounts for a major fraction of net new nitrogen input in terrestrial ecosystems. Transfer of fixed nitrogen to plant biomass is especially efficient via root nodule symbioses, which represent evolutionarily and ecologically specialized mutualistic associations. Frankia spp. (Actinobacteria), especially cluster II Frankia spp., have an extremely broad host range, yet comparatively little is known about the soil ecology of these organisms in relation to the host plants and their rhizosphere microbiomes. This study reveals a strong influence of the host plant on soil distribution of cluster II Frankia spp.

scholarly journals Phosphate Assimilation in Rhizobium(Sinorhizobium) meliloti: Identification of apit-Like Gene

1998 ◽  
Vol 180 (16) ◽  
pp. 4219-4226 ◽  
Author(s):  
Sylvie D. Bardin ◽  
Ralf T. Voegele ◽  
Turlough M. Finan
Keyword(s):  
Transport System ◽  
Sinorhizobium Meliloti ◽  
Rhizobium Meliloti ◽  
Root Nodules ◽  
Phosphate Transport ◽  
Wild Type ◽  
Transcription Start ◽  
Present Evidence ◽  
Suppressor Mutations ◽  
Mutant Cells

ABSTRACT Rhizobium meliloti mutants defective in thephoCDET-encoded phosphate transport system form root nodules on alfalfa plants that fail to fix nitrogen (Fix−). We have previously reported that two classes of second-site mutations can suppress the Fix− phenotype ofphoCDET mutants to Fix+. Here we show that one of these suppressor loci (sfx1) contains two genes, orfA and pit, which appear to form an operon transcribed in the order orfA-pit. The Pit protein is homologous to various phosphate transporters, and we present evidence that three suppressor mutations arose from a single thymidine deletion in a hepta-thymidine sequence centered 54 nucleotides upstream of the orfA transcription start site. This mutation increased the level of orfA-pit transcription. These data, together with previous biochemical evidence, show that theorfA-pit genes encode a Pi transport system that is expressed in wild-type cells grown with excess Pibut repressed in cells under conditions of Pi limitation. In phoCDET mutant cells, orfA-pitexpression is repressed, but this repression is alleviated by the second-site suppressor mutations. Suppression increasesorfA-pit expression compensating for the deficiencies in phosphate assimilation and symbiosis of the phoCDETmutants.

scholarly journals Loss of RNA Chaperone Hfq Unveils a Toxic Pathway in Pseudomonas aeruginosa

2019 ◽  
Vol 201 (20) ◽  
Author(s):  
Ian T. Hill ◽  
Thomas Tallo ◽  
Matthew J. Dorman ◽  
Simon L. Dove
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Opportunistic Pathogen ◽  
Toxic Effects ◽  
Growth Defect ◽  
Wild Type ◽  
Rna Chaperone ◽  
Small Protein ◽  
Content Type ◽  
Transcription Regulator ◽  
Mutant Cells

ABSTRACT Hfq is an RNA chaperone that serves as a master regulator of bacterial physiology. Here we show that in the opportunistic pathogen Pseudomonas aeruginosa, the loss of Hfq can result in a dramatic reduction in growth in a manner that is dependent upon MexT, a transcription regulator that governs antibiotic resistance in this organism. Using a combination of chromatin immunoprecipitation with high-throughput sequencing and transposon insertion sequencing, we identify the MexT-activated genes responsible for mediating the growth defect of hfq mutant cells. These include a newly identified MexT-controlled gene that we call hilR. We demonstrate that hilR encodes a small protein that is acutely toxic to wild-type cells when produced ectopically. Furthermore, we show that hilR expression is negatively regulated by Hfq, offering a possible explanation for the growth defect of hfq mutant cells. Finally, we present evidence that the expression of MexT-activated genes is dependent upon GshA, an enzyme involved in the synthesis of glutathione. Our findings suggest that Hfq can influence the growth of P. aeruginosa by limiting the toxic effects of specific MexT-regulated genes. Moreover, our results identify glutathione to be a factor important for the in vivo activity of MexT. IMPORTANCE Here we show that the conserved RNA chaperone Hfq is important for the growth of the opportunistic pathogen Pseudomonas aeruginosa. We found that the growth defect of hfq mutant cells is dependent upon the expression of genes that are under the control of the transcription regulator MexT. These include a gene that we refer to as hilR, which we show is negatively regulated by Hfq and encodes a small protein that can be toxic when ectopically produced in wild-type cells. Thus, Hfq can influence the growth of P. aeruginosa by limiting the toxic effects of MexT-regulated genes, including one encoding a previously unrecognized small protein. We also show that MexT activity depends on an enzyme that synthesizes glutathione.

scholarly journals Rhizobial Adaptation to Hosts, a New Facet in the Legume Root-Nodule Symbiosis

2010 ◽  
Vol 23 (6) ◽  
pp. 784-790 ◽  
Author(s):  
Marion Koch ◽  
Nathanaël Delmotte ◽  
Hubert Rehrauer ◽  
Julia A. Vorholt ◽  
Gabriella Pessi ◽  
...  
Keyword(s):  
Bradyrhizobium Japonicum ◽  
Root Nodule ◽  
Root Nodules ◽  
Host Adaptation ◽  
Host Recognition ◽  
Signal Molecules ◽  
Data Sets ◽  
Environmental Requirements ◽  
Applied Approach ◽  
Nodule Symbiosis

Rhizobia are able to infect legume roots, elicit root nodules, and live therein as endosymbiotic, nitrogen-fixing bacteroids. Host recognition and specificity are the results of early programming events in bacteria and plants, in which important signal molecules play key roles. Here, we introduce a new aspect of this symbiosis: the adaptive response to hosts. This refers to late events in bacteroids in which specific genes are transcribed and translated that help the endosymbionts to meet the disparate environmental requirements imposed by the hosts in which they live. The host-adaptation concept was elaborated with Bradyrhizobium japonicum and three different legumes (soybean, cowpea, and siratro). Transcriptomes and proteomes in root-nodule bacteroids were analyzed and compared, and genes and proteins were identified which are specifically induced in only one of the three hosts. We focused on those determinants that were congruent in the two data sets of host-specific transcripts and proteins: seven for soybean, five for siratro, and two for cowpea. One gene cluster for a predicted ABC-type transporter, differentially expressed in siratro, was deleted in B. japonicum. The respective mutant had a symbiotic defect on siratro rather than on soybean or cowpea. This result demonstrates the value of the applied approach and corroborates the host-specific adaptation concept.

scholarly journals The Drosophila Ortholog of MLL3 and MLL4 , trithorax related , Functions as a Negative Regulator of Tissue Growth

2013 ◽  
Vol 33 (9) ◽  
pp. 1702-1710 ◽  
Author(s):  
Hiroshi Kanda ◽  
Alexander Nguyen ◽  
Leslie Chen ◽  
Hideyuki Okano ◽  
Iswar K. Hariharan
Keyword(s):  
Histone H3 ◽  
Tissue Growth ◽  
Negative Regulator ◽  
Cyclin B ◽  
Wild Type ◽  
H3k4 Methylation ◽  
Content Type ◽  
Promote Cell Survival ◽  
Low Levels ◽  
Mutant Cells

The human MLL genes ( MLL1 to MLL4 ) and their Drosophila orthologs, trithorax ( trx ) and trithorax related ( trr ), encode proteins capable of methylating histone H3 on lysine 4. MLL1 and MLL2 are most similar to trx , while MLL3 and MLL4 are more closely related to trr . Several MLL genes are mutated in human cancers, but how these proteins regulate cell proliferation is not known. Here we show that trr mutant cells have a growth advantage over their wild-type neighbors and display changes in the levels of multiple proteins that regulate growth and cell division, including Notch, Capicua, and cyclin B. trr mutant clones display markedly reduced levels of H3K4 monomethylation without obvious changes in the levels of H3K4 di- and trimethylation. The trr mutant phenotype resembles that of Utx , which encodes a H3K27 demethylase, consistent with the observation that Trr and Utx are found in the same protein complex. In contrast to the overgrowth displayed by trr mutant tissue, trx clones are underrepresented, express low levels of the antiapoptotic protein Diap1, and exhibit only modest changes in global levels of H3K4 methylation. Thus, in Drosophila eye imaginal discs, Trr, likely functioning together with Utx, restricts tissue growth. In contrast, Trx appears to promote cell survival.

scholarly journals Cooperation, Competition, and Specialized Metabolism in a Simplified Root Nodule Microbiome

mBio ◽  
2020 ◽  
Vol 11 (4) ◽  
Author(s):  
Bridget L. Hansen ◽  
Rita de Cassia Pessotti ◽  
Monika S. Fischer ◽  
Alyssa Collins ◽  
Laila El-Hifnawi ◽  
...  
Keyword(s):  
Potential Role ◽  
Root Nodule ◽  
Root Nodules ◽  
Imaging Mass Spectrometry ◽  
In Planta ◽  
Content Type ◽  
Specialized Metabolites ◽  
Brevibacillus Brevis

ABSTRACT Microbiomes associated with various plant structures often contain members with the potential to make specialized metabolites, e.g., molecules with antibacterial, antifungal, or siderophore activities. However, when and where microbes associated with plants produce specialized metabolites, and the potential role of these molecules in mediating intramicrobiome interactions, is not well understood. Root nodules of legume plants are organs devoted to hosting symbiotic bacteria that fix atmospheric nitrogen and have recently been shown to harbor a relatively simple accessory microbiome containing members with the ability to produce specialized metabolites in vitro. On the basis of these observations, we sought to develop a model nodule microbiome system for evaluating specialized microbial metabolism in planta. Starting with an inoculum derived from field-grown Medicago sativa nodules, serial passaging through gnotobiotic nodules yielded a simplified accessory community composed of four members: Brevibacillus brevis, Paenibacillus sp., Pantoea agglomerans, and Pseudomonas sp. Some members of this community exhibited clear cooperation in planta, while others were antagonistic and capable of disrupting cooperation between other partners. Using matrix-assisted laser desorption ionization–imaging mass spectrometry, we found that metabolites associated with individual taxa had unique distributions, indicating that some members of the nodule community were spatially segregated. Finally, we identified two families of molecules produced by B. brevis in planta as the antibacterial tyrocidines and a novel set of gramicidin-type molecules, which we term the britacidins. Collectively, these results indicate that in addition to nitrogen fixation, legume root nodules are likely also sites of active antimicrobial production.

scholarly journals The LysR-Type Transcriptional Regulator CrgA Negatively Regulates the Flagellar Master Regulator flhDC in Ralstonia solanacearum GMI1000

2020 ◽  
Vol 203 (1) ◽  
Author(s):  
Xiaojing Fan ◽  
Zhiwen Zhao ◽  
Tingyan Sun ◽  
Wei Rou ◽  
Caiying Gui ◽  
...  
Keyword(s):  
Cell Motility ◽  
Ralstonia Solanacearum ◽  
Host Plants ◽  
Transcriptional Regulator ◽  
Growth Defect ◽  
Wild Type ◽  
Mobility Shift ◽  
Content Type ◽  
Gus Reporter ◽  
Electrophoretic Mobility Shift Assays

ABSTRACT The invasion and colonization of host plants by the destructive pathogen Ralstonia solanacearum rely on its cell motility, which is controlled by multiple factors. Here, we report that the LysR-type transcriptional regulator CrgA (RS_RS16695) represses cell motility in R. solanacearum GMI1000. CrgA possesses common features of a LysR-type transcriptional regulator and contains an N-terminal helix-turn-helix motif as well as a C-terminal LysR substrate-binding domain. Deletion of crgA results in an enhanced swim ring and increased transcription of flhDC. In addition, the ΔcrgA mutant possesses more polar flagella than wild-type GMI1000 and exhibits higher expression of the flagellin gene fliC. Despite these alterations, the ΔcrgA mutant did not have a detectable growth defect in culture. Yeast one-hybrid and electrophoretic mobility shift assays revealed that CrgA interacts directly with the flhDC promoter. Expressing the β-glucuronidase (GUS) reporter under the control of the crgA promoter showed that crgA transcription is dependent on cell density. Soil-soaking inoculation with the crgA mutant caused wilt symptoms on tomato (Solanum lycopersicum L. cv. Hong yangli) plants earlier than inoculation with the wild-type GMI1000 but resulted in lower disease severity. We conclude that the R. solanacearum regulator CrgA represses flhDC expression and consequently affects the expression of fliC to modulate cell motility, thereby conditioning disease development in host plants. IMPORTANCE Ralstonia solanacearum is a widely distributed soilborne plant pathogen that causes bacterial wilt disease on diverse plant species. Motility is a critical virulence attribute of R. solanacearum because it allows this pathogen to efficiently invade and colonize host plants. In R. solanacearum, motility-defective strains are markedly affected in pathogenicity, which is coregulated with multiple virulence factors. In this study, we identified a new LysR-type transcriptional regulator (LTTR), CrgA, that negatively regulates motility. The mutation of the corresponding gene leads to the precocious appearance of wilt symptoms on tomato plants when the pathogen is introduced using soil-soaking inoculation. This study indicates that the regulation of R. solanacearum motility is more complex than previously thought and enhances our understanding of flagellum regulation in R. solanacearum.

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