Draft Genome Sequence of
 Frankia
 sp. Strain CN3, an Atypical, Noninfective (Nod
 –
 ) Ineffective (Fix
 –
 ) Isolate from
 Coriaria nepalensis

Ghodhbane‐Gtari, Faten; Beauchemin, Nicholas; Bruce, David; Chain, Patrick; Chen, Amy; Davenport, Karen W.; Deshpande, Shweta; Detter, Chris; Furnholm, Teal; Goodwin, Lynne; Gtari, Maher; Han, Cliff; Han, James; Huntemann, Marcel; Ivanova, Natalia; Kyrpides, Nikos; Land, Miriam; Markowitz, Victor; Mavrommatis, Kostas; Nolan, Matt; Nouioui, Imen; Pagani, Ioanna; Pati, Amrita; Pitluck, Sam; Santos, Catarina L.; Sen, Arnab; Sur, Saubashya; Szeto, Ernest; Tavares, Fernando; Teshima, Hazuki; Thakur, Subarna; Wall, Luis Gabriel; Woyke, Tanja; Tisa, Louis S.

doi:10.1128/genomea.00085-13

Cited by 53 publications

(13 citation statements)

References 16 publications

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“…The fact that like Cluster I and Cluster III Frankia strains, these Cluster IV Frankia strains could be cultured suggests that their saprotrophic capabilities are broader than those of Cluster II strains. The genome sequence of one of these strains, CN3 [ 101 ] comprises 10 MB and represents the largest Frankia genome known to date, while being still in the range of the genome sizes of cluster III strains.…”

Section: Discussionmentioning

confidence: 99%

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

et al. 2015

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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 D. 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 D. 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 α- and β-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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Section: Discussionmentioning

confidence: 99%

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

et al. 2015

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“…Based on molecular phylogenetic analysis, four major clusters within the genus are recognized ( 5 – 8 ) and genomes for representatives from each cluster have been sequenced ( 9 – 24 ). Cluster I contains two subclusters: One subcluster (cluster Ia) represents Frankia strains with the ability to infect a wider range of host plants including member of the Betulaceae and Myricaceae families, and the other subcluster (cluster Ib) contains strains limited to Casuarina and Allocasuarina host plants.…”

Section: Genome Announcementmentioning

confidence: 99%

Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal

et al. 2016

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“…The fourth Frankia lineage consists of the "atypical" strains which are unable to reinfect actinorhizal host plants or form ineffective root nodule structures that are unable to fix nitrogen. Our understanding of this genus has been greatly enhanced by the sequencing of several Frankia genomes from the different Frankia lineages [24][25][26][27][28][29][30][31][32][33]. Analysis of Frankia genomes has revealed new potential with respect to metabolic diversity, natural product biosynthesis, and stress tolerance, which may help aid the cosmopolitan nature of the actinorhizal symbiosis [31,34].…”

Section: Frankia Genomics and Identification Of Metabolic Potentialmentioning

confidence: 99%

Frankia as a Biodegrading Agent

Rehan¹,

Swanson²,

Tisa³

2016

Actinobacteria - Basics and Biotechnological Applications

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The Frankia actinorhizal plant symbiosis plays an important role in colonization of soils contaminated with toxic aromatic hydrocarbons. Our understanding of the bacterial partner, Frankia, in the actinorhizal symbiosis has been greatly facilitated by the availability of sequenced genomes. The analysis of these Frankia genomes has suggested that these bacteria are metabolically diverse and have potential for toxic aromatic hydrocarbon degradation. In this chapter, we explore what is known about that metabolic potential.Keywords: Frankias-triazines, aromatic hydrocarbon degradation, P"H, bioremediation, bioinformatics, actinobacteria . IntroductionFrankia are filamentous nitrogen-fixing Gram-positive actinobacteria that are found as freeliving microbes in the soil and in symbiotic associations with actinorhizal plants [ -]. These bacteria fix nitrogen by converting atmospheric N into biologically useful ammonia and supply the host plants with a source of reduced nitrogen. Frankia are developmentally complex and form three cell types vegetative hyphae, spores located in sporangia, and vesicles. Hyphae are septate structures and form the growing state of this microbe. Under appropriate conditions, either terminal or intercalary multilocular sporangia are produced and contain many spores. When mature, the spores are released from the sporangia. The spores are presumed to aid in the survival and dispersal of Frankia in the environment. Vesicles are produced under nitrogen-limited conditions and consist of unique lipid-enveloped cellular structures that contain the enzymes responsible for nitrogen fixation. Thus, vesicles act as specialized structures for the nitrogen fixation process. Frankia are able to establish symbiotic nitrogen-© 2016 The Author(s). Licensee InTech. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.fixing associations with over species of woody dicotyledonous plants, termed actinorhizal plants, that are found in eight families of angiosperms [ , -]. The symbiosis with Frankia allows these actinorhizal host plants to colonize nutrient-poor soil and harsh environments. "ctinorhizal plants have been used to recolonize and reclaim industrial wastelands and environments contaminated with heavy metals and toxic aromatic hydrocarbon [ -]. The metabolic potential of these bacteria has only recently been investigated in the context of bioremediation [ -]. . . Frankia genomics and identification of metabolic potential"ased on phylogenetic analysis, Frankia strains have been classified into four main lineages [ -]. Members of lineage are found infective on host plants of the "etulaceae Alnus , Myricaceae, and Casuariaraceae families, while lineage represents strains that are infective on Rosaceae Dryas, etc. , Coriariaceae Coriaria , Datiscaceae Datisca , and the genus Ceanothus Rhamnaceae . Mem...

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Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod ^– ) Ineffective (Fix ^– ) Isolate from Coriaria nepalensis

Cited by 53 publications

References 16 publications

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal

Frankia as a Biodegrading Agent

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Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod – ) Ineffective (Fix – ) Isolate from Coriaria nepalensis

Cited by 53 publications

References 16 publications

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

Permanent Draft Genome Sequence for Frankia sp. Strain CeD, a Nitrogen-Fixing Actinobacterium Isolated from the Root Nodules of Casuarina equistifolia Grown in Senegal

Frankia as a Biodegrading Agent

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Draft Genome Sequence of Frankia sp. Strain CN3, an Atypical, Noninfective (Nod ^– ) Ineffective (Fix ^– ) Isolate from Coriaria nepalensis