The genomes of two nitrogen-fixing
Frankia
strains, Ag45/Mut15 and AgPM24, isolated from root nodules of
Alnus glutinosa
are described as representatives of a novel candidate species
.
Phylogenomic and ANI analyses confirmed that both strains are related to cluster 1 frankiae, and that both strains belong to a novel species. At 6.4 - 6.7 Mb, their genomes were smaller than those of other cultivated
Alnus
-infective cluster 1 strains but larger than that of the non-cultivated
Alnus
-infective cluster 1 Sp+ strain AgTrS that was their closest neighbor as assessed by ANI. Comparative genomic analyses identified genes essential for nitrogen-fixation, gene composition as regards COGs, secondary metabolites clusters and transcriptional regulators typical of those from
Alnus
-infective cluster 1 cultivated strains in both genomes. There were 459 genes present in other cultivated
Alnus
-infective strains lost in the two genomes, spread over the whole of the genome, which indicates genome erosion is taking place in these two strains.
KcsA, the bacterial K+ channel from Streptomyces lividans, is the prototypical model system to study the functional and structural correlations of the pore domain of eukaryotic voltage-gated K+ channels (Kv channels). It contains all the molecular elements responsible for ion conduction, activation, deactivation and inactivation gating[1]. KcsA’s structural simplicity makes it highly amenable for structural studies. Therefore, it is methodological advantageous to produce large amount of functional and properly folded KcsA in a cost-effective manner. In the present study, we show an optimized protocol for the over-expression and purification of large amount of high-quality, fully functional and crystallizable KcsA using inexpensive detergents, which significantly lowered the cost of the purification process.
The effect of host plants on the abundance and distribution of introduced and indigenous Frankia populations was assessed in soils and root nodules of four alder species, Alnus glutinosa, Alnus cordata, Alnus rubra and Alnus viridis. Plants were grown in microcosms with either a sandy soil without detectable frankiae, with or without inoculation of a mixture of Frankia isolates, or with a silty clay loam soil with indigenous Frankia. The presence of frankiae in soils increased plant height and root nodule formation, with significant increases in the presence of indigenous frankiae. Abundance in soils increased significantly for both introduced and indigenous Frankia populations independent of alder species, with generally largest increases in cluster 1b frankiae. Root nodules formed by introduced frankiae did not reflect the diversity of strains inoculated, with nodules generally only formed by strain ArI3 representing cluster 1a/d. All indigenous Frankia populations detected in soil were also found in A. glutinosa nodules, while A. cordata or A. rubra nodules contained different subsets of frankiae with unique abundances dependent on plant species. These results demonstrate the intrageneric differences of host plants in the selection of specific Frankia populations in soils for root nodule formation.
The genomes of two nitrogen-fixing
Frankia
strains, AgB32 and AgKG'84/4, were isolated from spore-containing (spore+) and spore-free (spore-) root nodules of
Alnus glutinosa
, but they did not sporulate upon reinfection. The two strains are described as representatives of two novel candidate species
.
Phylogenomic and ANI analyses indicate that each strain represents a novel species within cluster 1, with genome sizes of 6.3 and 6.7 Mb smaller than or similar to those of other cultivated
Alnus
-infective cluster 1 strains. Genes essential for nitrogen-fixation, clusters of orthologous genes, secondary metabolite clusters and transcriptional regulators analyzed by comparative genomic analyses were typical of those from
Alnus
-infective cluster 1 cultivated strains in both genomes. Compared to other cultivated
Alnus
-infective strains with large genomes, those of AgB32 and AgKG'84/4 had lost 380 or 409 genes, among which one
hup
cluster, one
shc
gene and the
gvp
cluster, which indicates genome erosion is taking place in these two strains.
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