( 2008 )
Reclassification of Rhodobium marinum and Rhodobium pfennigii as Afifella marina gen. nov. comb. nov. and Afifella pfennigii comb. nov., a new genus of photoheterotrophic Alphaproteobacteria and emended descriptions of Rhodobium, Rhodobium orientis and Rhodobium gokarnense.
PMID : 18774253 : DOI : 10.1016/j.syapm.2008.07.002
The isolation of photoheterotrophic organism C3 from a saline microbial mat led to its taxonomic characterization. Strain C3 could be identified as a member of the species Rhodobium marinum due to the genetic and phenotypic similarities to the type strain of the species (DSM 2698(T)). As a result of a taxonomic study, it was observed that the currently classified species of the genus formed two separate clades, each of them deserving genus status. Rhodobium orientis and Rhodobium gokarnense may be considered as true members of the genus Rhodobium, whereas R. marinum and Rhodobium pfennigii should be reclassified into a new genus. In the light of the genetic and phenotypic evidence observed, we propose that both latter species are reclassified within the new genus Afifella gen. nov., as species Afifella marina comb. nov., and Afifella pfennigii comb. nov., with Af. marina the type species of the genus. In addition, the taxonomic study has revealed that strain DSM 11549, identified as the type strain of the species Rhodopseudomonas julia, may represent a genomovar of Af. marina. The fact that the author of the first classification of R. julia indicates that the strains deposited in the German Collection for Microorganisms (DSM 11549) and American Collection of Type Cultures (ATCC 51105) do not correspond to the original description, makes the authenticity of the strains doubtful. Due to this reason, it is not proposed to reclassify the species.
( 2018 )
Crystal structure of afifavidin reveals common features of molecular assemblage in the bacterial dimeric avidins.
PMID : 30369031 : DOI : 10.1111/febs.14685
The subfamily of bacterial dimeric avidins is being extended through the discovery of additional members originating from diverse sources. All of these newly discovered dimeric avidin forms exhibit high affinity towards biotin, despite their lack of critical Trp in the classical tetrameric forms. The common feature of forming cylinder-like multimers (hexamers and octamers) seems to be more than a random occurrence, which generally characterizes their apo forms in the crystalline state and also in some cases in solution. Afifavidin from the Gram-negative �\-proteobacterium Afifella pfennigii is the fourth member of the subfamily of dimers, which, in the intact apo form, also congregates into octamers both in the solution and in the crystalline state, whereby the C-terminal extended segments stretch into the biotin-binding sites of adjacent non-canonical monomers. The intact apo afifavidin molecule self-assembles into toroid-shaped nanostructures that dissociate into the inherent dimers upon binding biotin. On removal of the C-terminal regions, the short-form of afifavidin forms dimers both in the solution and in the crystalline states. The high affinity of the dimeric forms of afifavidin towards biotin is maintained, due to the conserved disulfide bridge between L3,4 and L5,6 and the presence of Phe50 in L3,4 that compensate for the lack of the critical Trp in the tetrameric avidins. These cyclic multimeric-avidin assemblies may be exploited in the future to further diversify biotin-based nanotechnology or to serve as building blocks in the construction of bio-inspired materials. DATABASE: Structural data are available in the PDB databases under the accession numbers: 6HDV, 6HDS, 6HDT.