| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Carro, Lorena, et al.
(författare)
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Organic acids metabolism in Frankia alni
- 2016
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Ingår i: Symbiosis. - : Springer Science and Business Media LLC. - 0334-5114 .- 1878-7665. ; 70:1, s. 37-48
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Tidskriftsartikel (refereegranskat)abstract
- Trophic exchanges constitute the bases of the symbiosis between the nitrogen-fixing actinomycete Frankia and its host plant Alnus, but the identity of the compounds exchanged is still poorly known. In the current work, previously published transcriptomic studies of Alnus nodules and of symbiotic Frankia were reexamined for TCA cycle related genes. The bacterial TCA enzyme genes were all upregulated, especially the succinyl-CoA synthase and the citrate synthase while on the plant side, none was significantly modified in nodules relative to non-inoculated roots. A preliminary metabolomics approach permitted to see that citrate, 2-oxoglutarate, succinate, malate and fumarate were all more abundant (FC (Fold change) = 5-70) in mature nitrogen-fixing nodules than in roots. In the evaluation of the uptake and metabolism of these organic acids, a significant change was observed in the morphology of nitrogen fixing vesicles in vitro: the dicarboxylates malate, succinate and fumarate induced the formation of larger vesicles than was the case with propionate. Moreover, the production of spores was also modified depending on the organic acid present. The assays showed that most C4 dicarboxylates were taken up while C6 tricarboxylates were not and citrate even partially blocked catabolism of reserve carbon. Tests were performed to determine if the change in membrane permeability induced by Ag5, a peptide previously shown to modify the membranes of Frankia, increased the uptake of specific organic acids. No effect was observed with citrate while an increase in nitrogen fixation was seen with propionate.
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| 3. |
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| 4. |
- Herrera-Belaroussi, Aude, et al.
(författare)
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Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta
- 2020
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 43:6
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Tidskriftsartikel (refereegranskat)abstract
- We describe a new Frankia species, for three non-isolated strains obtained from Alnus glutinosa in France and Sweden, respectively. These strains can nodulate several Alnus species (A. glutinosa, A. incana, A. alno-betula), they form hyphae, vesicles and sporangia in the root nodule cortex but have resisted all attempts at isolation in pure culture. Their genomes have been sequenced, they are significantly smaller than those of other Alnus-infective species (5 Mb instead of 7.5 Mb) and are very closely related to one another (ANI of 100%). The name Candidatus Frankia nodulisporulans is proposed.
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| 5. |
- Leul, Melakeselam, et al.
(författare)
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The organization, regulation and phylogeny of uptake hydrogenase genes in Frankia
- 2007
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Ingår i: Physiologia Plantarum. - Copenhagen : Munksgaard. - 0031-9317 .- 1399-3054. ; 130:3, s. 464-470
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Tidskriftsartikel (refereegranskat)abstract
- Frankia alni ACN14a, Frankia sp. CcI3 and Frankia sp. EAN1pec, which have different host specificity and geographical distribution, have two uptake hydrogenase syntons in their genome: hydrogenase synton#1 and hydrogenase synton#2. The organization of hydrogenase genes on these syntons also varies. Phylogenetic analysis of the structural genes of these syntons showed that they were significantly divergent and that hydrogenase synton#1 subunits of these Frankia strains were probably ancestral among the actinobacteria. Hydrogenase gene duplication might have occurred long before emergence of the three Frankia lineages. The structural subunits of hydrogenase HupS2 and HupL2 (synton#2) of F. alni ACN14a and Frankia sp. CcI3, which belong to phylogenetic Frankia cluster 1, were grouped closely together but away from Frankia sp. EAN1pec, which belongs to Frankia cluster 3. Phylogenetic analysis showed the occurrence of lateral transfer of hupL2 in Frankia sp. EAN1pec to or from Geobacter sulfurreducens. The transcript levels of hupS1 and hupL1 relative to hupS2 and hupL2 were higher in F. alni ACN14a grown under free-living conditions. Under symbiotic conditions, transcript levels of hupS2 and hupL2 were higher than those of hupS1 and hupL1. Hydrogenase subunits of synton#1 are more expressed under free-living conditions, whereas those of synton#2 are mainly involved in symbiotic interactions.
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| 6. |
- Leul, Melakeselam, et al.
(författare)
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The phylogeny of uptake hydrogenases in Frankia
- 2009
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Ingår i: International Microbiology. - 1139-6709 .- 1618-1905. ; 12:1, s. 23-28
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Tidskriftsartikel (refereegranskat)abstract
- Uptake hydrogenase is an enzyme that is beneficial for nitrogen fixation in bacteria. Recent studies have shown that Frankia sp. has two sets of uptake hydrogenase genes, organized in synton 1 and synton 2. In the present study, phylogenetic analysis of the structural subunits of hydrogenase syntons 1 and 2 showed a distinct clustering pattern between the proteins of Frankia strains that were isolated from different host plants and non-Frankia organisms. The structural subunits of hydrogenase synton 1 of Frankia sp. CpI1, Frankia alni ACN14a, and F. alni AvCI1 were grouped together while those of Frankia spp. CcI3, KB5, UGL140104, and UGL011102 formed another group. The structural subunits of hydrogenase synton 2 of F. alni ACN14a and Frankia spp. CcI3 and BCU110501 grouped together, but those of Frankia spp. KB5 and CpI1, F. alni ArI3, and F. alniAvCI1 comprised a separate group. The structural subunits of hydrogenase syntons 1 and 2 of Frankia sp. EAN1pec were more closely related to those of non-Frankia bacteria, i.e., Streptomyces avermitilis and Anaeromyxobacter sp., respectively, than to those of other Frankia strains, suggesting the occurrence of lateral gene transfer between these organisms. In addition, the accessory Hyp proteins of hydrogenase syntons 1 and 2 of F. alni ACN14a and Frankia sp. CcI3 were shown to be phylogenetically more related to each other than to those of Frankia EAN1pec.
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| 7. |
- Normand, Philippe, et al.
(författare)
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Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
- 2007
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051. ; 17:1, s. 7-15
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Tidskriftsartikel (refereegranskat)abstract
- Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N2-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%–98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
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| 8. |
- Normand, Philippe, et al.
(författare)
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Proposal of 'Candidatus Frankia californiensis', the uncultured symbiont in nitrogen-fixing root nodules of a phylogenetically broad group of hosts endemic to western North America
- 2017
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Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 67:10, s. 3706-3715
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Tidskriftsartikel (refereegranskat)abstract
- The genus Frankia comprises a group of nitrogen-fixing actinobacteria that form root-nodule symbioses with perennial dicotyledonous plants in the nitrogen-fixing clade. These bacteria have been characterized phylogenetically and grouped into four clusters (clusters 1-4). Cluster 2 contains mostly uncultured strains that induce nodules on species of the genera Datisca (Datiscaceae), Coriaria (Coriariaceae), Ceanothus (Rhamnaceae) and several genera in the family Rosaceae (Cercocarpus, Chamaebatia, Dryas, Purshia), all of which except members of the genus Coriaria are present within the California Floristic Province (CFP) or neighbouring areas of western North America. Those strains occurring in western North America are genetically very closely related to one another, and genetically distinct from strains characterized from other locales. We hereby propose to create a 'Candidatus Frankia californiensis' species for those cluster 2 strains of the genus Frankia with both high genetic similarity and a geographical distribution in or near the CFP.
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| 9. |
- Persson, Tomas, et al.
(författare)
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Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant
- 2015
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Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 10:5
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Tidskriftsartikel (refereegranskat)abstract
- Frankia strains are nitrogen-fixing soil actinobacteria that can form root symbioses with actinorhizal plants. Phylogenetically, symbiotic frankiae can be divided into three clusters, and this division also corresponds to host specificity groups. The strains of cluster II which form symbioses with actinorhizal Rosales and Cucurbitales, thus displaying a broad host range, show suprisingly low genetic diversity and to date can not be cultured. The genome of the first representative of this cluster, Candidatus Frankia datiscae Dg1 (Dg1), a microsymbiont of Datisca glomerata, was recently sequenced. A phylogenetic analysis of 50 different housekeeping genes of Dg1 and three published Frankia genomes showed that cluster II is basal among the symbiotic Frankia clusters. Detailed analysis showed that nodules of Datisca glomerata, independent of the origin of the inoculum, contain several closely related cluster II Frankia operational taxonomic units. Actinorhizal plants and legumes both belong to the nitrogen-fixing plant clade, and bacterial signaling in both groups involves the common symbiotic pathway also used by arbuscular mycorrhizal fungi. However, so far, no molecules resembling rhizobial Nod factors could be isolated from Frankia cultures. Alone among Frankia genomes available to date, the genome of Dg1 contains the canonical nod genes nodA, nodB and nodC known from rhizobia, and these genes are arranged in two operons which are expressed in Datisca glomerata nodules. Furthermore, Frankia Dg1 nodC was able to partially complement a Rhizobium leguminosarum A34 nodC::Tn5 mutant. Phylogenetic analysis showed that Dg1 Nod proteins are positioned at the root of both alpha- and beta-rhizobial NodABC proteins. NodA-like acyl transferases were found across the phylum Actinobacteria, but among Proteobacteria only in nodulators. Taken together, our evidence indicates an Actinobacterial origin of rhizobial Nod factors.
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| 10. |
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| 11. |
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| 12. |
- Persson, Tomas, et al.
(författare)
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The N-metabolites of roots and actinorhizal nodules from Alnus glutinosa and Datisca glomerata : can D-glomerata change N-transport forms when nodulated?
- 2016
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Ingår i: Symbiosis. - : Springer Science and Business Media LLC. - 0334-5114 .- 1878-7665. ; 70:1, s. 149-157
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Tidskriftsartikel (refereegranskat)abstract
- To gain more insight in nitrogen metabolism in actinorhizal nodules, a comparison between the N metabolite profiles in roots vs. nodules was initiated for one host plant from the best-examined order of actinorhizal plants, Fagales, A. glutinosa (Betulaceae), a temperate tree, and one host plant from the Cucurbitales order, Datisca glomerata (Datiscaceae). For both symbioses, the symbiotic transcriptomes have been published and can be used to assess the expression of genes representing specific metabolic pathways in nodules. The amino acid profiles of roots in this study suggest that A. glutinosa transported aspartate, glutamate and citrulline in the xylem, a combination of nitrogenous solutes not published previously for this species. The amino acid profiles of D. glomerata roots depended on whether the plants were nodulated or grown on nitrate; roots of nodulated plants contained increased amounts of arginine. Although bacterial transcriptome data showed no symbiotic auxotrophy for branched chain amino acids (leucine, isoleucine, valine) in either symbiosis, D. glomerata nodules contained comparatively high levels of these amino acids. This might represent a response to osmotic stress.
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| 13. |
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| 14. |
- Santos, Catarina L, et al.
(författare)
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Modulation of Frankia alni ACN14a oxidative stress response: activity, expression and phylogeny of catalases
- 2007
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Ingår i: Physiologia Plantarum. - : Wiley. - 0031-9317 .- 1399-3054. ; 130, s. 454-463
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Tidskriftsartikel (refereegranskat)abstract
- The finding that an oxidative burst was a general phenomenon in the response of hosts challenged by various symbiotic or pathogenic microbes has stimulated increasing interest in investigating the enzymology of antioxidant protection in bacteria. The question of whether the antioxidant mechanisms have been a decisive evolutionary driving force for the nitrogen-fixing microsymbiont Frankia spp. is still open. In this study, Frankia alni strain ACN14a, which is a mid-range infective strain, was used as a model to explore the basal oxidative stress response in terms of enzymatic activity, relative expression and phylogeny. Non-denaturing polyacrylamide gels stained for catalatic activity revealed the presence of two monofunctional catalases KatA and KatB (EC number 1.11.1.6), which activity was shown to increase when the cells were challenged with the oxidants H2O2 and methyl viologen. Real-time RT-PCR targeting the two genes showed a consistent increase in the number of transcripts when the RNA was extracted from oxidative stress-induced cells. Comparison between the expression and the activity data suggests that posttranscriptional mechanisms might be involved in the regulation of catalases in F. alni. Furthermore, upstream of katA, a fur gene coding for a ferric uptake regulator was found, forming a gene pair that functionally resembles the conserved actinobacterial synton fur–katG, which contains a gene coding for a catalase–peroxidase. Phylogenetic analysis of the F. alni fur–katA synton suggests that this genomic organization was the result of genome reshuffling events.
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| 15. |
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| 16. |
- Zhang, Yu, et al.
(författare)
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Comparative phylogenomics and phylotranscriptomics provide insights into the genetic complexity of nitrogen-fixing root-nodule symbiosis
- 2024
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Ingår i: Plant communications. - 2590-3462. ; 5:1
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Tidskriftsartikel (refereegranskat)abstract
- Plant root-nodule symbiosis (RNS) with mutualistic nitrogen-fixing bacteria is restricted to a single clade of angiosperms, the Nitrogen-Fixing Nodulation Clade (NFNC), and is best understood in the legume family. Nodulating species share many commonalities, explained either by divergence from a common ancestor over 100 million years ago or by convergence following independent origins over that same time period. Regardless, comparative analyses of diverse nodulation syndromes can provide insights into constraints on nodulation-what must be acquired or cannot be lost for a functional symbiosis-and the latitude for variation in the symbiosis. However, much remains to be learned about nodulation, especially outside of legumes. Here, we employed a large-scale phylogenomic analysis across 88 species, complemented by 151 RNA-seq libraries, to elucidate the evolution of RNS. Our phylogenomic analyses further emphasize the uniqueness of the transcription factor NIN as a master regulator of nodulation and identify key mutations that affect its function across the NFNC. Comparative transcriptomic assessment revealed nodulespecific upregulated genes across diverse nodulating plants, while also identifying nodule-specific and nitrogen-response genes. Approximately 70% of symbiosis-related genes are highly conserved in the four representative species, whereas defense-related and host-range restriction genes tend to be lineage specific. Our study also identified over 900 000 conserved non-coding elements (CNEs), over 300 000 of which are unique to sampled NFNC species. NFNC-specific CNEs are enriched with the active H3K9ac mark and are correlated with accessible chromatin regions, thus representing a pool of candidate regulatory elements for genes involved in RNS. Collectively, our results provide novel insights into the evolution of nodulation and lay a foundation for engineering of RNS traits in agriculturally important crops.
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