Alpha/beta‐hydrolases: A unique structural motif coordinates catalytic acid residue in 40 protein fold families

The alpha/beta‐hydrolases are a family of acid‐base‐nucleophile catalytic triad enzymes with a common fold, but using a wide variety of substrates, having different pH optima, catalyzing unique catalytic reactions and often showing improved chemical and thermo stability. The ABH enzymes are prime targets for protein engineering. Here, we have classified active sites from 51 representative members of 40 structural ABH fold families into eight distinct conserved geometries. We demonstrate the occurrence of a common structural motif, the catalytic acid zone, at the catalytic triad acid turn. We show that binding of an external ligand does not change the structure of the catalytic acid zone and both the ligand‐free and ligand‐bound forms of the protein belong to the same catalytic acid zone subgroup. We also show that the catalytic acid zone coordinates the position of the catalytic histidine loop directly above its plane, and consequently, fixes the catalytic histidine in a proper position near the catalytic acid. Finally, we demonstrate that the catalytic acid zone plays a key role in multi‐subunit complex formation in ABH enzymes, and is involved in interactions with other proteins. As a result, we speculate that each of the catalytic triad residues has its own supporting structural scaffold, similar to the catalytic acid zone, described above, which together form the extended catalytic triad motif. Each scaffold coordinates the function of its respective catalytic residue, and can even compensate for the loss of protein function, if the catalytic amino acid is mutated.     

A Novel Method to Analyze Social Transmission in Chronologically Sequenced Assemblages,Implemented on Cultural Inheritance of the Art of Cooking

Here we present an analytical technique for the measurement and evaluation of changes in chronologically sequenced assemblages. To illustrate the method, we studied the cultural evolution of European cooking as revealed in seven cook books dispersed over the past 800 years. We investigated if changes in the set of commonly used ingredients were mainly gradual or subject to fashion fluctuations. Applying our method to the data from the cook books revealed that overall, there is a clear continuity in cooking over the ages – cooking is knowledge that is passed down through generations, not something (re-)invented by each generation on its own. Looking at three main categories of ingredients separately (spices, animal products and vegetables), however, disclosed that all ingredients do not change according to the same pattern. While choice of animal products was very conservative, changing completely sequentially, changes in the choices of spices, but also of vegetables, were more unbounded. We hypothesize that this may be due a combination of fashion fluctuations and changes in availability due to contact with the Americas during our study time period. The presented method is also usable on other assemblage type data, and can thus be of utility for analyzing sequential archaeological data from the same area or other similarly organized material.     

Involvement of Azopirillum brasilense plasmid DNA in the productio of indole acetic acid

Indole acetic acid (IAA) production in Azospirillum brasilense strain Sp245 is controlled by a 85 MDa plasmid naturally present in this bacterium. In the presence of L-tryptophan, anthranilic acid production and almost no IAA production occurs in a derivative strain harbouring a Tn5-Mob insertion in the 85 MDa plasmid. Agrobacterium tumefaciens strain GM19023, upon transfer of Tn5-Mob labelled 85 MDa plasmid of A. brasilense Sp245, gains the ability to produce anthranilic acid.     

The extracranial arterial system in the heads of beaked whales,with implications on diving physiology and pathogenesis

Beaked whales are medium‐sized toothed whales that inhabit depths beyond the continental shelf; thus beaked whale strandings are relatively infrequent compared to those of other cetaceans. Beaked whales have been catapulted into the spotlight by their tendency to strand in association with naval sonar deployment. Studies have shown the presence of gas and fat emboli within the tissues and analysis of gas emboli is suggestive of nitrogen as the primary component. These findings are consistent with human decompression sickness (DCS) previously not thought possible in cetaceans. Because, tissue loading with nitrogen gas is paramount for the manifestation of DCS and nitrogen loading depends largely on the vascular perfusion of the tissues, we examined the anatomy of the extracranial arterial system using stranded carcasses of 16 beaked whales from five different species. Anatomic regions containing lipid and/or air spaces were prioritized as potential locations of nitrogen gas absorption due to the known solubility of nitrogen in adipose tissue and the nitrogen content of air, respectively. Attention was focused on the acoustic fat bodies and accessory sinus system on the ventral head. We found much of the arterial system of the head to contain arteries homologous to those found in domestic mammals. Robust arterial associations with lipid depots and air spaces occurred within the acoustic fat bodies of the lower jaw and pterygoid air sacs of the ventral head, respectively. Both regions contained extensive trabecular geometry with small arteries investing the trabeculae. Our findings suggest the presence of considerable surface area between the arterial system, and the intramandibular fat bodies and pterygoid air sacs. Our observations may provide support for the hypothesis that these structures play an important role in the exchange of nitrogen gas during diving. J. Morphol. 277:5–33, 2016. © 2015 Wiley Periodicals, Inc.     

Substitution of two histidine residues in YadA protein of Yersinia enterocolitica abrogates collagen binding, cell adherence and mouse virulence

The plasmid-encoded surface protein YadA of Yersinia enterocolitica mediates binding to diverse extracellular matrix (ECM) proteins, adherence to epithelial cell lines, resistance to complement lysis, autoagglutination, and is required for mouse virulence. Using site-directed mutagenesis we attempted to analyse the relationship between structural domains and functions of YadA. In a first approach we could abrogate collagen binding by chemical modification of histidyl residues of YadA protein. This result prompted us to substitute histidyl residues (His) of conserved regions of YadA protein of Y. enterocolitica 08 by tyrosine residues using site-directed mutagenesis. Substitution of His-156 and His-159 (YadA-2 mutant) resulted in abrogation of binding to ECM proteins, of cell adherence, and in reduction of mouse virulence, whereas autoagglutination, serum complement resistance and oligomer formation remained unaffected. A striking result was obtained from the orogastric mouse-infection model: the YadA-2 mutant retained the ability to colonize the small intestine and to invade and multiply within the Peyer's patches but was impaired in colonizing mesenteric lymph nodes and spleen in comparison to the wild-type strain.     

Microbody phosphoglycerate kinase of Trypanosoma brucei: expression and complementation in Escherichia coli

In the primitive eukaryotic parasite, Trypanosoma brucei, most of the enzymes of glycolysis are located within microbody organelles called glycosomes. Proteins destined for the glycosome are synthesized on free ribosomes and post-translationally translocated into the organelle. The gene, gPGK, encoding the glycosomal isozyme of phosphoglycerate kinase (gPGK), was cloned adjacent to a T7 promoter and cotransformed with a plasmid encoding T7 RNA polymerase into Escherichia coli Pgk-cells. Functional complementation occurred, but only after the creation of a ribosome-binding site by mutagenesis. This represents the first example of complementation of an E. coli mutant with a gene encoding a microbody protein. Enzymatically active recombinant gPGK was purified to near homogeneity by ion exchange chromatography from highly expressing E. coli. The recombinant protein will aid in studies of glycosomal biogenesis.