Biochemistry (Moscow) (v.79, #7)

Age-related obesity is a heritage of the evolutionary past by E. V. Tereshina; S. I. Ivanenko (581-592).
In the process of human aging, an increase in the total amount of fat is observed mainly due to accumulation of lipids in non-adipose tissues. Insulin resistance, provoked by the intracellular accumulation of triglycerides, is often associated with development of such age-related diseases as atherosclerosis, type 2 diabetes, cancer, osteoporosis, and also with systemic inflammation and lipo- and glucose toxicity. Accumulation of lipids and lipophilic compounds is a biological phenomenon common for both prokaryotes and eukaryotes. Initially, it arose as an adaptation to starvation and shortage of nitrogen-containing nutrients, but later it converted into a depot of membrane material, needed on recommencement of cell division. In rodents and humans, the accumulation of non-metabolized fat in non-adipose tissues can be regarded as an adaptation to changes in the internal medium on a certain stage of ontogenesis as a result of age-related dysfunction of adipose tissue.
Keywords: lipid accumulation; adaptation; adipose tissue; lipotoxicity; aging

Data are presented on a variety of intracellular structures of the vegetative hyphae of the filamentous fungus Neurospora crassa and the involvement of these structures in the tip growth of the hyphae. Current ideas on the molecular and genetic mechanisms of tip growth and regulation of this process are considered. On the basis of comparison of data on behaviors of mitochondria and microtubules and data on the electrical heterogeneity of the hyphal apex, a hypothesis is proposed about a possible supervisory role of the longitudinal electric field in the structural and functional organization of growing tips of the N. crassa hyphae.
Keywords: Neurospora crassa ; tip growth; interaction of intracellular structures; electrical heterogeneity of hypha

Nuclear matrix and structural and functional compartmentalization of the eucaryotic cell nucleus by S. V. Razin; V. V. Borunova; O. V. Iarovaia; Y. S. Vassetzky (608-618).
Becoming popular at the end of the 20th century, the concept of the nuclear matrix implies the existence of a nuclear skeleton that organizes functional elements in the cell nucleus. This review presents a critical analysis of the results obtained in the study of nuclear matrix in the light of current views on the organization of the cell nucleus. Numerous studies of nuclear matrix have failed to provide evidence of the existence of such a structure. Moreover, the existence of a filamentous structure that supports the nuclear compartmentalization appears to be unnecessary, since this function is performed by the folded genome itself.
Keywords: nuclear matrix; chromatin; functional compartmentalization of cell nucleus; architecture of interphase chromosomes; interchromatin domain; DNA loops

Secondary biochemical and morphological consequences in lysosomal storage diseases by J. Alroy; C. Garganta; G. Wiederschain (619-636).
More than 50 hereditary lysosomal storage disorders (LSDs) are currently described. Most of these disorders are due to a deficiency of certain hydrolases/glycosidases and subsequent accumulation of nonhydrolyzable carbohydrate-containing compounds in lysosomes. Such accumulation causing hypertrophy of the lysosomal compartment is a characteristic feature of affected cells in LSDs. The investigation of biochemical and cellular parameters is of particular interest for understanding “life” of lysosomes in the normal state and in LSDs. This review highlights the wide spectrum of biochemical and morphological changes during developing LSDs that are extremely critical for many metabolic processes inside the various cells and tissues of affected persons. The data presented will help establish new complex strategies for metabolic correction of LSDs.
Keywords: lysosomes; lysosomal storage diseases; autophagy; pathogenic cascades; recycling; deficiency of lysosomal enzymes and protein cofactors; metabolic correction

Selective inhibitor of histone deacetylase 6 (tubastatin A) suppresses proliferation of hepatitis C virus replicon in culture of human hepatocytes by M. V. Kozlov; A. A. Kleymenova; K. A. Konduktorov; A. Z. Malikova; S. N. Kochetkov (637-642).
Acetylation of α-tubulin was studied in cultures of human hepatocytes under the influence of selective inhibitors of histone deacetylases HDAC6 and SIRT-2 — tubastatin A and 2-(3-phenethoxyphenylamino)benzamide, respectively. It was found that in hepatocyte cell line HepG2 acetylated α-tubulin is accumulated preferentially on inhibition of HDAC6 but not of SIRT-2. Under the same conditions, no acetylation of α-tubulin was observed in hepatocyte cell line Huh7. However, the inhibition of HDAC6 with tubastatin A led to hyperacetylation of α-tubulin and simultaneously to decrease in viral RNA concentration in hepatocyte cell line Huh7-luc/neo, which supports propagation of the full genome replicon of hepatitis C virus. The correlation between these two processes points to HDAC6 as a promising cellular target for therapy of hepatitis C.
Keywords: human hepatocytes; acetylation of α-tubulin; HDAC6 and SIRT-2; hepatitis C virus replicon

Cation-pi interactions at non-redundant protein-RNA interfaces by Honggucun Zhang; Chunhua Li; Feng Yang; Jiguo Su; Jianjun Tan; Xiaoyi Zhang; Cunxin Wang (643-652).
Cation-pi interactions have proved to be important in proteins and protein-ligand complexes. Here, cation-pi interactions are analyzed for 282 non-redundant protein-RNA interfaces. The statistical results show that this kind of interactions exists in 65% of the interfaces. The four RNA bases are ranked as Gua > Ade > Ura > Cyt according to their propensity to participate in cation-pi interactions. The corresponding ranking for the involved amino acid residues is: Arg > Lys > Asn > Gln. The same trends are obtained based on the empirical energy calculation. The Arg-Gua pairs have the greatest stability and are also most frequently observed. The number of cation-pi pairs involving unpaired bases is 2.5 times as many as those involving paired bases. Hence, cation-pi interactions show sequence and structural specificities. For the bicyclic bases, Gua and Ade, their 5-atom rings participate in cation-pi interactions somewhat more than the 6-atom rings, with percentages of 54 and 46%, respectively, which is due to the higher cation-pi participation proportion (63%) of 5-atom rings in the paired bases. These results give a general view of cation-pi interactions at protein-RNA interfaces and are helpful in understanding the specific recognition between protein and RNA.
Keywords: cation-pi interactions; protein-RNA interfaces; sequence and structural specificities; electrostatic energy; ab initio

Caenorhabditis elegans eyes absent ortholog EYA-1 Is required for stress resistance by Bing-ying Wang; Xue-song Xu; Yu-xiao Cui; Hua Wang; Ge Liu; Zhizhuang Joe Zhao; Jun-feng Ma; Xue-qi Fu (653-662).
Eyes absent (Eya) is a highly conserved transcription cofactor and protein phosphatase that regulates multiple developmental processes throughout the metazoans. It is a dual function protein, working as a transcription factor in the nucleus and as a tyrosine phosphatase in the cytoplasm. In this study, we isolated EYA-1 of Caenorhabditis elegans, the only homolog of Eyes absent, and set up an effective feeding-based RNAi (RNA interference) against the gene. We found that knockdown of EYA-1 decreased heat and oxidative stress tolerance and accelerated the onset of paralysis mediated by Aβ1-42 proteotoxicity and polyQ. Under heat stress (35°C), EYA-1 knockdown shortened the mean lifespan by 16.8%, which could be attributed to decrease in heat shock protein-16.2 (hsp-16.2) expression. Under oxidative stress, EYA-1 knockdown could shorten the mean lifespan by 18.7%, which could be attributed to intracellular ROS accumulation and the decrease of superoxide dismutase-3 (sod-3) protein expression. Moreover, EYA-1 knockdown animals also showed increased lipofuscin accumulation under oxidative stress. Further studies demonstrated that EYA-1 knockdown could not inhibit daf-16 nuclear accumulation in wild-type worms in response to stress. On the other hand, EYA-1 deficiency did not further reduce stress resistance of daf-16 mutants, which are stress sensitive. Quantitative real-time PCR results also showed that the expression of two daf-16 target genes, hsp-12.3 and sod-3, was downregulated in EYA-1 RNAi-treated worms under stress. All this evidence indicates EYA-1 is required for stress resistance of worms, and it might act downstream of daf-16 to regulate expression of stress resistance-associated genes.
Keywords: EYA-1; Caenorhabditis elegans ; RNA interference; stress resistance

The purpose of the present study was to examine changes in preadipocytes following the coculture of preadipocytes and adipocytes and the effects on the secretion of adipocytes and macrophages following induction of inflammation and insulin resistance. Mature adipocytes and RAW264.7 macrophages were treated with lipopolysaccharide and insulin to establish models of inflammation and insulin resistance, respectively. The mRNA expression levels of IL-6, MCP-1, and TNF-α in all adipocyte treatment groups were significantly greater compared with the control, and that of adiponectin was less (P < 0.05). In the RAW264.7 macrophages, the mRNA expression levels of IL-6 and TNF-α were greater than those in the control group (P < 0.05). Moreover, the results of this study confirmed that adipocytes and macrophages increased the secretion of inflammatory factors under conditions of induced inflammation and insulin resistance. In addition, 3T3-L1 adipocytes inhibited the proliferation and differentiation of preadipocytes when cocultured with adipocytes under conditions of inflammation and/or insulin resistance, and the phenotype of preadipocytes did not change.
Keywords: insulin resistance; adipocytes; preadipocytes; adipokines

Functional attributes of recombinant CtCBM35 (family 35 carbohydrate binding module) of β-mannanase of family 26 Glycoside Hydrolase from Clostridium thermocellum were deduced by biochemical and in silico approaches. Ligand-binding analysis of expressed CtCBM35 analyzed by affinity-gel electrophoresis and fluorescence spectroscopy exhibited association constants K a ∼ 1.2·105 and 3.0·105 M−1 with locust bean galactomannan and mannotriose, respectively. However, CtCBM35 showed low ligand-binding affinity with insoluble ivory nut mannan with K a of 5.0·10−5 M−1. Unfolding transition analysis by fluorescence spectroscopy explained the conformational changes of CtCBM35 in the presence of guanidine hydrochloride (5 M) and urea (6.25 M). This explained that CtCBM35 has good conformational stability and requires higher free energy of denaturation to invoke unfolding. The three-dimensional (3-D) model of CtCBM35 from C. thermocellum generated by Modeller9v8 displayed predominance of β-sheets arranged as β-jelly-roll fold. The secondary structure of CtCBM35 by PredictProtein showed the presence of two α-helices (3%), 12 β-sheets (45%), and 15 random coils (52%). Secondary structural element analysis of cloned, expressed, and purified recombinant CtCBM35 by circular dichroism also corroborated the in silico predicted secondary structure. Multiple sequence alignment of CtCBM35 showed conserved residues (Tyr123, Gly124, and Phe125), which are commonly observed in mannan specific CBMs. Docking analysis of CtCBM35 with manno-oligosaccharide displayed the involvement of Tyr26, Gln29, Asn43, Trp66, Tyr68, Leu69, Arg76, and Leu127 residues, making polar contact with the ligand molecules. Ligand docking analysis of CtCBM35 exhibiting higher binding affinity with mannotriose and galactomannan (Man-Gal-Man moiety) substantiated the affinity binding and fluorescence results, displaying similar values of K a.
Keywords: CtCBM35; homology modeling; docking; CD spectra; affinity electrophoresis; fluorescence spectra; unfolding transition

The effects of detergents, trypsin, and bivalent metal ions on production of phosphatidic and lysophosphatidic acids by the action of phospholipase D (PLD) on lecithin and lysolecithin were studied. It was found that these reaction products and dodecyl sulfate ions activate PLD, whereas other anionic detergents are less effective. A protective effect of the functioning enzyme against its hydrolytic inactivation by trypsin was found. Bivalent metal ions can be arranged in the following sequence by their ability to activate PLD in the hydrolysis of lecithin and lysolecithin: Ca2+ > Sr2+ > Ba2+ > Mg2+. These results are considered in relation to a proposed mechanism of activation and functioning of PLD with the participation of clusters of phosphatidates and lysophosphatidates. Such Me2+-induced formation of rafts or microdomains from the products of hydrolysis of phospholipids can rationalize not only PLD activation and self-regulation, but also the action of this mechanism on other components and properties of biomembranes. PLD and other lipolytic enzymes can be classified as lateral vector enzymes.
Keywords: phospholipase D; detergents; trypsin; metal ions; phosphatidates; lysophosphatidates; activation; function; regulation; biomembranes

Study of effect of substitution of the penultimate amino acid residue on expression, structure, and functional properties of Yersinia pseudotuberculosis OmpY porin by T. F. Solov’eva; N. M. Tischenko; V. A. Khomenko; O. Y. Portnyagina; N. Y. Kim; G. N. Likhatskaya; O. D. Novikova; M. P. Isaeva (694-705).
The purpose of the study was to compare the expression of two Yersinia pseudotuberculosis proteins, wild-type porin OmpY and the mutant porin OmpY designated as OmpY-Q having the uncharged amino acid residue Gln instead of positively charged Arg at the penultimate position in the same heterologous host. According to the literature, a similar substitution (Lys to Gln) of the penultimate amino acid residue in Neisseria meningitidis porin PorA drastically improved the assembly of the protein in the E. coli outer membrane in vivo. Site-directed mutagenesis was used to replace Arg by Gln (R338Q) in OmpY, and the conditions for optimal expression and maturation of OmpY-Q were selected. It was found that the growth rates of E. coli strains producing OmpY and OmpY-Q and the expression levels of the porins were approximately equal. Comparative analysis of recombinant OmpY and OmpY-Q did not show significant differences in structure, antigenic, and functional properties of the porins, or any noticeable effect of the R338Q substitution in OmpY on its assembly in the E. coli outer membrane in vivo. The probable causes of discrepancies between our results and the previous data on porin PorA are discussed considering the known mechanisms of biogenesis of porins at the periplasmic stage.
Keywords: Yersinia pseudotuberculosis ; outer membrane; pore-forming proteins; site-directed mutagenesis; biogenesis of porins; spatial structure; computer modeling

The most popular strategy for normalization of RT-qPCR data involves presenting them in comparison with expression of “housekeeping” genes. However, the required stable expression of the control genes is not always achievable. As an alternative, we used ribonucleoprotein phage particles as an exogenous internal control and demonstrated that this type of normalization provides a simple and reliable method for quantification in RT-qPCR experiments. Using phage-based normalization, we analyzed mRNA levels of three popular housekeeping genes coding β-actin, glyceraldehyde-3-phosphate dehydrogenase, and ribosomal protein L30 and showed high variability in their expression patterns during rat brain development, indicating that they should not be used as controls in gene expression studies of the developing brain either individually or in combination. Using phage-based controls, we showed interstrain differences and age-related changes in the expression of genes involved in proteoglycan biosynthesis and degradation in developing brain of senescenceaccelerated OXYS rats and control Wistar rats.
Keywords: PCR data normalization; reference genes; housekeeping genes; exogenous internal control; ribonucleoprotein particles; senescence-accelerated OXYS rats

RNA-binding properties of the plant protein Nt-4/1 by S. S. Makarova; A. G. Solovyev; S. Y. Morozov (717-726).
The tobacco α-helical protein Nt-4/1 with unknown function forms ribonucleoprotein (RNP) complexes in vitro. Results obtained by retardation of RNP complexes in agarose gel were confirmed by Western-Northern hybridization. Several deletion and point mutants of Nt-4/1 were constructed, and the RNA-binding site was mapped in a positively charged region of the C-terminal domain of the protein. The results of this study and those described earlier support our hypothesis of the participation of Nt-4/1 protein in spreading RNA-containing pathogens in the plant.
Keywords: protein Nt-4/1; potato spindle tuber viroid; RNA binding

Regulation of glucokinase activity in liver of hibernating ground squirrel Spermophilus undulatus by L. Ya. Khu; K. B. Storey; A. M. Rubtsov; N. Yu. Goncharova (727-732).
The kinetic properties of glucokinase (GLK) from the liver of active and hibernating ground squirrels Spermophilus undulatus have been studied. Entrance of ground squirrels into hibernation from their active state is accompanied by a sharp decrease in blood glucose (Glc) level (from 14 to 2.9 mM) and with a significant (7-fold) decrease of GLK activity in the liver cytoplasm. Preparations of native GLK practically devoid of other molecular forms of hexokinase were obtained from the liver of active and hibernating ground squirrels. The dependence of GLK activity upon Glc concentration for the enzyme from active ground squirrel liver showed a pronounced sigmoid character (Hill coefficient, h = 1.70 and S 0.5 = 6.23 mM; the experiments were conducted at 25°C in the presence of enzyme stabilizers, K+ and DTT). The same dependence of enzyme activity on Glc concentration was found for GLK from rat liver. However, on decreasing the temperature to 2°C (simulation of hibernation conditions), this dependency became almost hyperbolic (h = 1.16) and GLK affinity for substrate was reduced (S 0.5 = 23 mM). These parameters for hibernating ground squirrels (body temperature 5°C) at 25°C were found to be practically equal to the corresponding values obtained for GLK from the liver of active animals (h = 1.60, S 0.5 = 9.0 mM, respectively); at 2°C sigmoid character was less expressed and affinity for Glc was drastically decreased (h = 1.20, S 0.5 = 45 mM). The calculations of GLK activity in the liver of hibernating ground squirrels based on enzyme kinetic characteristics and seasonal changes in blood Glc concentrations have shown that GLK activity in the liver of hibernating ground squirrels is decreased about 5500-fold.
Keywords: glucokinase; hexokinase; cooperative properties; hibernation; ground squirrel Spermophilus undulatus