Cold Shock Domain Proteins: Structure and Interaction with Nucleic Acids.

This review summarizes the features of cold shock domain (CSD) proteins in the context of their interactions with nucleic acids and describes similarities and differences in the structure of cold shock proteins of prokaryotes and CSD proteins of eukaryotes with special emphasis on the functions related to the RNA/DNA-binding ability of these proteins. The mechanisms and specificity of their interaction with nucleic acids in relation to the growing complexity of protein domain structure are described, as well as various complexes of the mammalian Y-box binding protein 1 (YB-1) with nucleic acids (filaments, globules, toroids). The role of particular amino acid residues in the binding of nitrogenous bases and the sugar-phosphate backbone of nucleic acids is emphasized. The data on the nucleic acid sequences recognized by the Y-box binding proteins are systematized. Post-translational modifications of YB-1, especially its phosphorylation, affect the recognition of specific sequences in the promoter regions of various groups of genes by YB-1 protein. The data on the interaction of Lin28 protein with let-7 miRNAs are summarized. The features of the domain structure of plant CSD proteins and their effect on the interaction with nucleic acids are discussed.

How Fucose of Blood Group Glycotopes Programs Human Gut Microbiota.

Formation of appropriate gut microbiota is essential for human health. The first two years of life is the critical period for this process. Selection of mutualistic microorganisms of the intestinal microbiota is controlled by the FUT2 and FUT3 genes that encode fucosyltransferases, enzymes responsible for the synthesis of fucosylated glycan structures of mucins and milk oligosaccharides. In this review, the mechanisms of the selection and maintenance of intestinal microorganisms that involve fucosylated oligosaccharides of breast milk and mucins of the newborn's intestine are described. Possible reasons for the use of fucose, and not sialic acid, as the major biological signal for the selection are also discussed.

Erratum to: "How Fucose of Blood Group Glycotypes Programs Human Gut Microbiota" [Biochemistry (Moscow), 82, 973 (2017)].

This corrects the article DOI: 10.1134/S0006297917090012.

[Analysis of the efficiency of antimicrobial treatment for community-acquired pneumonia in clinical practice]. / Analiz éffektivnosti antimikrobnoi terapii vnebol'nichnoi pnevmonii v klinicheskoi praktike.

AIM: To analyze actual drug consumption based on the defined daily dose (DDD analysis) and to analyze the utilization of drugs based on their proportion of the total defined daily doses (DU90% analysis) for the antimicrobial therapy of community-acquired pneumonia (CAP) in clinical practice at a hospital in Russia. MATERIAL AND METHODS: The investigation materials were the data of 117 case histories of male (51.3%) and female (48.7%) patients hospitalized with CAP at Nizhny Novgorod City Clinical Hospital Five in 2015. The investigation enrolled all the patients admitted to the hospital over the analyzed period. DDD analysis and DU90% analysis were used as study methods. RESULTS: DDD analysis and DU90% analysis of antimicrobial therapy for CAP were carried out at the hospital in clinical practice during a year. The annual number of defined daily doses (NDDD) for antimicrobial drugs, the number of defined daily doses per 100 bed-days (NDDD/100 bed-days), and a drug load (g) per 1000 CAP patients per day and per CAP patient per year were determined. The largest NDDD/year for CAP treatment with ceftriaxone was 376 g, or 43.43 NDDD/100 bed-days, which is much higher than that with other antimicrobial agents. The daily drug load of ceftriaxone per 1,000 CAP patients was 8.8 g, which exceeds that of moxifloxacin by 18.7 times, azithromycin and levofloxacin by 5 times, and ampicillin/sulbactam by 2.3 times. The daily drug load of ceftriaxone per CAP patient was 3.2 g, which exceeds that of of ampicillin/sulbactam by 2.3 times, levofloxacin and azithromycin by 5 times, and moxifloxacin by 19 times. CONCLUSION: It may be recommended that the proportion of cephalosporins as drugs that promote the rise of resistance in microbes and their production of extended-spectrum ß-lactamases should be further limited, the proportion of penicillins be extended, and the administered ampicillin/sulbactam be added, for example, by amoxicillin/clavulanate. Penicillins contribute to the rise of resistance to a lesser degree, and the use of two different penicillin molecules specified in the guidelines for the treatment of CAP will be able to slow the process further. By the same reasoning, it is also advisable to use cefuroxime (second-generation cephalosporins) along with ceftriaxone in patients in stable condition, without impairing vital functions.

[The concept of risk factors in assessing the impact of smoking on an exacerbation of chronic obstructive pulmonary disease].

AIM: By using the risk concept, to determine a quantitative relationship between smoking in patients with chronic obstructive pulmonary disease (COPD) and the development of an exacerbation. SUBJECTS AND METHODS: Case history data were studied in 166 patients admitted for a COPD exacerbation in 2009 to 2012. There were 2 exacerbations for a year or longer. The patients were divided into 2 groups: smokers (n=110) and nonsmokers (n=56). The concept for estimating the risks was based on the calculation of absolute risk in the exposed and unexposed groups, attributable risk, relative risk, and population attributable risk and on the determination of standard errors for each type of risk and confidence interval. RESULTS: The methodological aspects of determining the quantitative relationship between smoking in patients with COPD and the development of its exacerbations (twice or more per year) were considered on the basis of the statistical concept of risk factors. A risk factor concept-based analysis has shown that the impact of smoking is directly related to the worsening of COPD. The frequency of exacerbations is 71.8% in the group of smoking patients and 32.1 % in that of nonsmoking patients; the risk factor increases the likelihood of this event by 39.7%. CONCLUSION: Smoking leads to a 2.2-fold increase in the frequency of COPD exacerbations. The potential hazard index was 2.5.

[Membrane technologies in medicine and ecology].

The paper considers the state-of-the-art of membrane technologies, as applied to the needs of medicine and ecology, the major benefits of membranes for microfiltration and ultrafiltration, and perspectives for the application of new membranes based on new materials. A number of membranes based on aromatic polyamide imides (PAs) have been investigated using rotavirus models. Due to the good solubility of PAs in amide solvents, their based asymmetric membranes can be formed in one step, by applying a water setting bath. The one-stage procedure developed at the Institute of High Molecular Compounds, Russian Academy of Sciences, for the synthesis of aromatic PAs allows one to prepare polymers with required viscosity and strength characteristics. This gives rise to a membrane as porous films of digitiform morphology and asymmetric porous structure.

[Detection of C-P-lyase activity in a cell-free extract of Escherichia coli].

A system has been developed for in vitro testing of E. coli C-P-lyase (the enzyme cleaving C-P bonds in phosphonates). NADH, ATP, and the system of ATP regeneration were necessary but not sufficient for expression of the C-P-lyase activity in cell-free extracts of E. coli. Experimental evidence suggests that glucose 6-phosphate and (or) glucose activate C-P-lyase, serving as precursors in the formation of (alkylphosphono)ribose, an intermediate in the reaction. Guanine is the most likely acceptor of the phosphate group.

Phosphonates and their degradation by microorganisms.

Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond. Wide occurrence of phosphonates among xenobiotics polluting the environment has aroused interest in pathways and mechanisms of their biodegradation. Only procaryotic microorganisms and the lower eucaryotes are capable of phosphonate biodegradation via several pathways. Destruction of the non-activated C-P bond by the C-P lyase pathway is of fundamental importance, and understanding of the process is a basic problem of biochemistry and physiology of microorganisms. This review offers analysis of available data on phosphonate-degrading microorganisms, degradation pathways, and genetic and physiological regulation of this process.

Effect of export-specific cytoplasmic chaperone, protein SecB, on secretion of Escherichia coli alkaline phosphatase.

The efficiency of secretion of Escherichia coli alkaline phosphatase depends on the presence in cells of a cytoplasmic chaperone--protein SecB. Secretion increases in the presence of this chaperone at 30 degrees C, which is the most favorable for the interaction of SecB with the export-initiation domain found previously in the N-terminal region of the mature enzyme. This interaction most likely occurs in the region of the export domain, which is located close to the signal peptide and in complex with a translocational ATPase--protein SecA.

The primary structure of the N-terminal region of mature alkaline phosphatase is critical for secretion and function of the enzyme.

The export signal has been assumed to be localized not only in the signal peptide of a secreted protein precursor, but also in the N-terminal region of the mature polypeptide chain. Mutant alkaline phosphatases with amino acid substitutions of two positively charged residues (Lys or Arg) in this region at different distances from the signal peptide have been studied to test this assumption. The efficiency of secretion has been shown to decrease in mutant proteins with amino acid substitutions in the region of 16-18 amino acid residues; the closer to the signal peptide is the substitution, the greater is the decrease. A change in the primary structure of the N-terminal domain results also in an increase in the Michaelis constant, which is greater the farther is the amino acid substitution from the signal peptide, suggesting a change in the enzyme function as well.

Secretory heat-shock protein of the thermotolerant yeast Hansenula polymorpha. Identification and comparative characteristics.

Thirteen investigated strains of ascomycetous yeasts able to produce secretory heat-shock proteins (sHSPs) do not response equally to a high temperature by induction of the synthesis and secretion of these proteins. In this respect the above yeasts can be divided into three groups having a positive (I), a negative (II), and an indefinite reaction (III) to the heat shock. The thermotolerant yeast Hansenula polymorpha belongs to the first group. In this yeast heat shock induces the synthesis and secretion of sHSP gp280. This new representative differs from known sHSPs in molecular mass and subunit composition. In other respects (glycosylation, mainly extracellular localization, and the character of export into the culture medium) it displays similar properties.

Extracellular glycoprotein specific for Saccharomyces sensu stricto.

Using affinity-purified rabbit polyclonal antibodies against an extracellular mannoprotein (gp400) of Saccharomyces cerevisiae, the presence of immunohomologic proteins with similar electrophoretic mobility was shown in the culture medium of S. bayanus, S. paradoxus and S. pastorianus. Cross-reactive bands with different electrophoretic behaviour were observed for S. dairensis, S. exiguus, S. kluyveri, S. unisporus and also for the species moved from Saccharomyces to Arxiozyma, Kluyveromyces, Pachytichospora, Torulaspora and Zygosaccharomyces, in contrast to ascosporous yeasts of other genera in which these proteins were not found.

Identification of a novel secreted glycoprotein of the yeast Saccharomyces cerevisiae stimulated by heat shock.

A new secreted yeast glycoprotein with an Mr of about 400 kDa (gp400) has been found. The glycoprotein is an O-mannosylated oligomer, whose synthesis and export into culture medium are stimulated by heat shock. Intracellular transport of gp400 is carried out by membrane vesicles distinct from the known constitutive secretory vesicles. Immunological analysis revealed gp400 only in Saccharomyces species.

[Differences in the catalytic properties of fragments of the ceruloplasmin molecule]. / Razlichiia v kataliticheskikh svoistvakh fragmentov molekuly tseruloplazmina.

Human ceruloplasmin (Cp) molecule is split into fragments by a contaminating protease upon storage of enzyme preparations. These fragments were separated by SDSPAAG electrophoresis and their Mr were estimated. Separate fragments were subjected to immunoelectrophoresis in agarose gel containing rabbit antibodies to human Cp. The immunoprecipitation peaks were then specifically stained to reveal the oxidase activity of the fragments towards o-dianisidine and L-cysteine. All the fragments were able to oxidize the latter, however, only the whole Cp molecule and the two of its largest fragments could oxidize the former. It seems likely that oxidation of L-cysteine does not require the presence of several copper ions constituting the catalytic centre of the blue oxidase (Cp.). contrarily, o-dianisidine seems to be oxidized by the multicopper active site of the enzyme rather than by the autonomously acting singular copper(s). Since o-dianisidine is oxidized by the fragments of Cp lacking the C-terminal polypeptide, which was thought to bind all the coppers of the active centre, it was assumed that some of the latter are bound by amino acids located in another part of the molecule.