The ribosome as an allosterically regulated molecular machine

The ribosome as a complex molecular machine undergoes significant conformational rearrangements during the synthesis of polypeptide chains of proteins. In this review, information obtained using various experimental methods on the internal consistency of such rearrangements is discussed. It is demonstrated that allosteric regulation involves all the main stages of the operation of the ribosome and connects functional elements remote by tens and even hundreds of angstroms. Data obtained using Förster resonance energy transfer (FRET) show that translocation is controlled in general by internal mechanisms of the ribosome, and not by the position of the ligands. Chemical probing data revealed the relationship of such remote sites as the decoding, peptidyl transferase, and GTPase centers of the ribosome. Nevertheless, despite the large amount of experimental data accumulated to date, many details and mechanisms of these phenomena are still not under- stood. Analysis of these data demonstrates that the development of new approaches is necessary for deciphering the mech- anisms of allosteric regulation of the operation of the ribosome.     

Small nucleolar RNAs and their genes in vertebrates

Genes of box C/D small nucleolar RNAs (snoRNAs) were searched for in the genomes of members of all classes of vertebrates that do not belong to placental mammals. A tendency for an increase in the number of copies of snoRNA genes was observed in such vertebrates. This trend was most pronounced in anamnia (amphibians and fish). Box C mutations were found in 14 snoRNAs in all gene copies among all species studied. The role of the described events is discussed.     

Dynamics of abundance of antifungal strains of Pseudomonas in the rhizosphere of hydroponic cucumbers grown on greenhouse mineral substrate

Data were obtained on the dynamics of the abundance of the biocontrol strains of Pseudomonas chlororaphis SPB1217 and Pseudomonas fluorescens SPB2137 with antifungal activity. These strains are able to develop in the rhizosphere of cucumbers grown on mineral substrate under hydroponic conditions in industrial greenhouses. After four weeks of vegetation of plants, the abundance of the inoculated strains was 19–28% of the total bacterial numbers determined by inoculation onto solid medium. The investigated strains spread together with the young, actively growing and exudating roots; they reached a stable level of abundance in deep layers of the greenhouse substrate. A significant difference in the abundance of fungi in the tested variants was observed after 20 days of vegetation: the abundance of fungi in the control was two times higher than in the variant inoculated with strain SPB2137.     

The production of toxic shock syndrome toxins and enterotoxins by Staphylococcus aureus]

The production of toxins of the toxic shock syndrome and enterotoxins by S. aureus of clinical origin was studied by means of commercial standard antisera and standard toxins. The study revealed that among 511 strains isolated in Russia toxigenic ones constituted 41%, and among 592 strains isolated in Czechia toxigenic ones constituted 63%. The capacity for producing toxins may be used as an epidemiological marker.     

The role of PAR1 in protective action of activated protein C during nonimmune activation of mast cells

Activated protein C (APC) regulates the functional activity of mast cells by reducing release of β-hexosaminidase, the marker of mast cell degranulation. APC modulated not only spontaneous secretion from mast cells, but also secretion induced by the degranulators, proteinase-activated receptor agonist peptide (PAR1-AP) and compound 48/80. PAR1 desensitization by thrombin abolished the decrease of β-hexosaminidase secretion induced by low APC concentrations (≤1.5 nM). APC inactivated by phenylmethylsulfonyl fluoride (PMSF), did non mimic the enzyme action on mast cells. Duodenase (the duodenal proteinase) activated peritoneal mast cell via PAR1. APC abolished the proinflammatory effect of duodenase and PAR1-AP by reducing release of mast cell mediators. The effect of APC could be attributed to nitric oxide generation by mast cells because in the presence of L-NAME the secretory function restored. These data suggest involvement of mast cell PAR1 into regulatory mechanism responsible for the anti-inflammatory effect of APC.     

The Zn-peptidase superfamily: functional convergence after evolutionary divergence.

Zn-dependent carboxypeptidases (ZnCP) cleave off the C-terminal amino acid residues from proteins and peptides. Here we describe a superfamily that unites classical ZnCP with other enzymes, most of which are known (or likely) to participate in metal-dependent peptide bond cleavage, but not necessarily in polypeptide substrates. It is demonstrated that aspartoacylase (ASP gene) and succinylglutamate desuccinylase (ASTE gene) are members of the ZnCP family. The Zn-binding site along with the structural core of the protein is shown to be conserved between ZnCP and another large family of hydrolases that includes mostly aminopeptidases (ZnAP). Both families (ZnCP and ZnAP) include not only proteases but also enzymes that perform N-deacylation, and enzymes that catalyze N-desuccinylation of amino acids. This is a result of functional convergence that apparently occurred after the divergence of the two families.