Arthrobacter polaris sp. nov., a new cold-adapted member of the family Micrococcaceae isolated from Antarctic fellfield soil.

An aerobic, Gram-stain-positive and non-spore-forming strain, designated C1-1T, was isolated from a fellfield soil sample collected from frost-sorted polygons on Jane Col, Signy Island, Maritime Antarctic. Cells with a size of 0.65-0.9×1.2-1.7 µm have a flagellar motile apparatus and exhibit a rod-coccus growth cycle. Optimal growth conditions were observed at 15-20 °C, pH 7.0 and NaCl concentration up to 0.5 % (w/v) in the medium. The 16S rRNA gene sequence of C1-1T showed the highest pairwise similarity of 98.77 % to Arthrobacter glacialis NBRC 113092T. Phylogenetic trees based on the 16S rRNA and whole-genome sequences revealed that strain C1-1T belongs to the genus Arthrobacter and is most closely related to members of the 'Arthrobacter psychrolactophilus group'. The G+C content of genomic DNA was 58.95 mol%. The original and orthologous average nucleotide identities between strain C1-1T and A. glacialis NBRC 113092T were 77.15 % and 77.38 %, respectively. The digital DNA-DNA relatedness values between strain C1-1T and A. glacialis NBRC 113092T was 21.6 %. The polar lipid profile was composed mainly of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified glycolipid. The predominant cellular fatty acids were anteiso-C15 : 0 (75 %) and anteiso-C17 : 0 (15.2 %). Menaquinone MK-9(H2) (86.4 %) was the major respiratory quinone in strain C1-1T. The peptidoglycan type was determined as A3α (l-Lys-l-Ala3; A11.6). Based on all described phylogenetic, physiological and chemotaxonomic characteristics, we propose that strain C1-1T (=DSM 112353T=CCM 9148T) is the type strain of a novel species Arthrobacter polaris sp. nov.

Effect of temperature on the compositions of ladderane lipids in globally surveyed anammox populations.

The adaptation of bacteria involved in anaerobic ammonium oxidation (anammox) to low temperatures will enable more efficient removal of nitrogen from sewage across seasons. At lower temperatures, bacteria typically tune the synthesis of their membrane lipids to promote membrane fluidity. However, such adaptation of anammox bacteria lipids, including unique ladderane phospholipids and especially shorter ladderanes with absent phosphatidyl headgroup, is yet to be described in detail. We investigated the membrane lipids composition (UPLC-HRMS/MS) and dominant anammox populations (16S rRNA gene amplicon sequencing, Fluorescence in situ hybridization) in 14 anammox enrichments cultivated at 10-37 °C. "Candidatus Brocadia" appeared to be the dominant organism in all but two laboratory enrichments of "Ca. Scalindua" and "Ca. Kuenenia". At lower temperatures, the membranes of all anammox populations were composed of shorter [5]-ladderane ester (reduced chain length demonstrated by decreased fraction of C20/(C18 + C20)). This confirmed the previous preliminary evidence on the prominent role of this ladderane fatty acid in low-temperature adaptation. "Ca. Scalindua" and "Ca. Kuenenia" had distinct profile of ladderane lipids compared to "Ca. Brocadia" biomasses with potential implications for adaptability to low temperatures. "Ca. Brocadia" membranes contained a much lower amount of C18 [5]-ladderane esters than reported in the literature for "Ca. Scalindua" at similar temperature and measured here, suggesting that this could be one of the reasons for the dominance of "Ca. Scalindua" in cold marine environments. Furthermore, we propose additional and yet unreported mechanisms for low-temperature adaptation of anammox bacteria, one of which involves ladderanes with absent phosphatidyl headgroup. In sum, we deepen the understanding of cold anammox physiology by providing for the first time a consistent comparison of anammox-based communities across multiple environments.

The first structure-function study of GH151 α-l-fucosidase uncovers new oligomerization pattern, active site complementation, and selective substrate specificity.

Fucosylated compounds are abundantly present in nature and are associated with many biological processes, therefore carrying great potential for use in medicine and biotechnology. Efficient ways to modify fucosylated compounds are still being developed. Promising results are provided by glycosyl hydrolases with transglycosylating activities, such as α-l-fucosidase isoenzyme 2 from Paenibacillus thiaminolyticus (family GH151 of Carbohydrate-Active enZYmes). Currently, there is no 3D structure representing this glycoside hydrolase family and only a few members have been investigated. Here, we present the first structure-function study of a GH151 member, providing the key insights into its specific oligomerization and active site properties. According to the crystal structure, small-angle X-ray scattering data and catalytic investigation, this enzyme functions as a tetramer of a new type and represents the second known case of active site complementation among all α-l-fucosidases. Mutation of the active site-complementing residue histidine 503 to alanine confirmed its influence on α-l-fucosidase activity and, specifically, on substrate binding. Several unique features of GH151 family α-l-fucosidases were revealed, including the oligomerization pattern, active site accessibility and complementation, and substrate selectivity. Some common properties of GH151 glycosyl hydrolases then would be the overall three-domain structure and conservation of the central domain loop 2 function, including its complementation role and the formation of the carbohydrate-binding platform in the active site vicinity.

Active site complementation and hexameric arrangement in the GH family 29; a structure-function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus.

α-l-Fucosidase isoenzyme 1 from bacterium Paenibacillus thiaminolyticus is a member of the glycoside hydrolase family GH29 capable of cleaving l-fucose from nonreducing termini of oligosaccharides and glycoconjugates. Here we present the first crystal structure of this protein revealing a novel quaternary state within this family. The protein is in a unique hexameric assembly revealing the first observed case of active site complementation by a residue from an adjacent monomer in this family. Mutation of the complementing tryptophan residue caused changes in the catalytic properties including a shift of the pH optimum, a change of affinity to an artificial chromogenic substrate and a decreased reaction rate for a natural substrate. The wild-type enzyme was active on most of the tested naturally occurring oligosaccharides and capable of transglycosylation on a variety of acceptor molecules, including saccharides, alcohols or chromogenic substrates. Mutation of the complementing residue changed neither substrate specificity nor the preference for the type of transglycosylation acceptor molecule; however, the yields of the reactions were lower in both cases. Maltose molecules bound to the enzyme in the crystal structure identified surface carbohydrate-binding sites, possibly participating in binding of larger oligosaccharides.