Biochemistry (Moscow) (v.74, #2)

TATA box polymorphisms in human gene promoters and associated hereditary pathologies by L. K. Savinkova; M. P. Ponomarenko; P. M. Ponomarenko; I. A. Drachkova; M. V. Lysova; T. V. Arshinova; N. A. Kolchanov (117-129).
TATA-binding protein (TBP) is the first basal factor that recognizes and binds a TATA box on TATA-containing gene promoters transcribed by RNA polymerase II. Data available in the literature are indicative of admissible variability of the TATA box. The TATA box flanking sequences can influence TBP affinity as well as the level of basal and activated tran-scription. The possibility of mediated involvement in in vivo gene expression regulation of the TBP interactions with variant TATA boxes is supported by data on TATA box polymorphisms and associated human hereditary pathologies. A table containing data on TATA element polymorphisms in human gene promoters (about 40 mutations have been described), associated with particular pathologies, their short functional characteristics, and manifestation mechanisms of TATA-box SNPs is presented. Four classes of polymorphisms are considered: TATA box polymorphisms that weaken and enhance promoter, polymorphisms causing TATA box emergence and disappearance, and human virus TATA box polymorphisms. The described examples are indicative of the polymorphism-associated severe pathologies like thalassemia, the increased risk of hepatocellular carcinoma, sensitivity to H. pylori infection, oral cavity and lung cancers, arterial hypertension, etc.
Keywords: TATA box; gene expression; SNP; hereditary pathologies

Possible involvement of NO in the stimulating effect of pifithrins on survival of hemopoietic clonogenic cells by S. Ya. Proskuryakov; A. G. Konoplyannikov; O. A. Konoplyannikova; L. I. Shevchenko; Yu. G. Verkhovskii; A. F. Tsyb (130-136).
Pifithrin α (PFTα), one of the first known low molecular weight modulators of activity of tumor suppressor p53, increases survival of hemopoietic clonogenic cells (evaluated by the criterion of formation of endogenous spleen CFU-C8 colonies in irradiated animals). This effect appeared when PFTα was administered either before or after irradiation. Increase in CFU-C8 was also observed after administration of two PFTα analogs, derivatives of 2-amino-4,5,6,7-tetrahy-drobenzothiazole. These included a parent compound, 2-ATBT (2-amino-4,5,6,7-tetrahydrobenzothiazole), which is used for synthesis of PFTα, and a product of its intramolecular cyclization under physiological conditions, cyclo-PFT (2-(4-methylphenyl)imidazo[2,1-b]-5,6,7,8-tetrahydrobenzothiazole). Earlier we found that many low molecular weight compounds increasing number of CFU-C8 (e.g. isothiourea derivatives) demonstrate NO inhibitory activity. Such activity was also found in 2-ATBT and cyclo-PFT by means of EPR spectroscopy of NO. These compounds caused more than twofold inhibition of NO production in vivo. Thus, it has been demonstrated that PFTα and its structural analogs increase survival of hemopoietic clonogenic cells in vivo, and NO may play a role in the mechanism of this effect.
Keywords: pifithrin α; cyclo-pifithrin; hemopoietic clonogenic cells; endogenous spleen colonies; nitric oxide production; EPR spectroscopy of NO spin trap

D-Amino acid oxidase (DAAO) is an FAD-dependent enzyme that metabolizes D-amino acids in microbes and animals. However, such ability has not been identified in plants so far. We predicted a complete DAAO coding sequence consisting of 1158 bp and encoding a protein of 386 amino acids. We cloned this sequence from the leaf cDNA population of maize plants that could utilize D-alanine as a nitrogen source and grow normally on media containing D-Ala at the concentrations of 100 and 1000 ppm. For more understanding of DAAO ability in maize plant, we produced a recombinant plasmid by the insertion of isolated cDNA into the pMALc2X Escherichia coli expression vector, downstream of the maltose-binding protein coding sequence. The pMALc2X-DAAO vector was used to transform the TB1 strain of E. coli cells. Under normal growth conditions, fused DAAO (with molecular weight of about 78 kDa) was expressed up to 5 mg/liter of bacterial cells. The expressed product was purified by affinity chromatography and subjected to in vitro DAAO activity assay in the presence of five different D-amino acids. Fused DAAO could oxidize D-alanine and D-aspartate, but not D-leucine, D-isoleucine, and D-serine. The cDNA sequence reported in this paper has been submitted to EMBL databases under accession number AM407717.
Keywords: D-amino acid oxidase; D-amino acids; Zea mays ; flavoenzyme; overexpression

H1 histone modulates DNA hydrolysis with WEN1 and WEN2 endonucleases from wheat coleoptiles by L. I. Fedoreyeva; T. A. Smirnova; G. Ya. Kolomijtseva; B. F. Vanyushin (145-152).
We show that total H1 histone from wheat seedlings or rat liver enhances hydrolysis of λ phage DNA with plant endonucleases WEN1 and WEN2 isolated from wheat coleoptiles. Optimal DNA/protein weight ratio in the hydrolysis reaction is 1: 1. The action of fractions I and IV (obtained from total wheat H1 histone by electrophoresis) on DNA hydrolysis with WEN1 and WEN2 enzymes depends on the DNA methylation status. Fraction IV of wheat histone H1 stimulates hydrolysis of unmethylated λ phage DNA with WEN1 and WEN2 enzymes. Hydrolysis of methylated λ phage DNA (it contains 5-methylcytosine in Cm5CWGG sequences and N6-methyladenine in Gm6ATC sites) with WEN1 is inhibited with fractions I and IV of wheat H1 histone. Fractions II and III of wheat H1 histone do not influence DNA hydrolysis with WEN1 and WEN2. S-Adenosyl-L-methionine (SAM) stimulates activity of these plant enzymes. But in the presence of H1 histone, SAM does not add to the ability of the enzyme to hydrolyze more DNA compared with that induced with H1 histone itself. Therefore, the stimulating effects of SAM and H1 histone on DNA hydrolysis with plant endonucleases may be similar. It could be suggested that SAM and H1 histone can induce more or less analogous allosteric transformations in the structure of the investigated plant endonucleases. Thus, DNA hydrolysis with plant endonucleases is modulated with total H1 histone. H1 histone fractions affect DNA hydrolysis in a different fashion; they enhance or inhibit hydrolysis depending on the DNA methylation status. We suggest that H1 histone changes site specificity of endonucleases or it might be responsible for formation of new or masking of old sites available for these enzymes due to changes in DNA structure induced in a DNA-histone complex.
Keywords: apoptosis; plant; H1 histone; endonucleases; DNA methylation; DNA fragmentation

One-dimensional proteomic mapping of human liver cytochromes P450 by A. V. Lisitsa; N. A. Petushkova; I. P. Nikitin; V. G. Zgoda; I. I. Karuzina; S. A. Moshkovskii; O. V. Larina; O. G. Skipenko; L. O. Polyschuk; H. Thiele; A. I. Archakov (153-161).
A method for constructing one-dimensional proteomic maps (1D-PM) based on mass spectrometric identification of proteins from adjacent slices of one-dimensional electrophoregram has been developed. For the proteomic mapping, gel lanes were sectioned into slices less than 0.2 mm thick and each slice was subjected to enzymatic hydrolysis. The resultant mixture of peptide fragments was analyzed by matrix-assisted laser desorption time-of-flight mass spectrometry (MALDI-TOF) and liquid chromatography electrospray ionization tandem mass spectrometry (LC-MS/MS). Proteins were identified by the mass spectra obtained. Data on peptide fragments and corresponding identified proteins were presented as a 1D-PM. Proteomic maps were constructed by assigning individual proteins to gel slices based on number of matching peptides in a corresponding MS-data. On 1D-PM of human liver microsomal fraction, 18 proteins were identified in the region of 40–65 kDa. These included 12 membrane proteins belonging to the superfamily of cytochromes P450. Pooling of mass spectrometric data, obtained from several adjacent gel slices (molecular zooming) increased sequence coverage of CYP2A (cytochrome P450 family 2A). The maximal coverage of 66% significantly exceeded the level of 48% that could be obtained using one (even the most informative) slice. This method can be applied to the proteomic profiling of membrane-bound proteins.
Keywords: proteomics; one-dimensional gel electrophoresis; molecular zooming; mass spectrometry; membrane-bound protein identification

Adsorption chromatography of proteins by V. I. Surovtsev; V. M. Borzenkov; K. V. Detushev (162-164).
A method for adsorption chromatography of proteins is proposed. A protein solution is passed through a cellulose column at a pH value corresponding to an isoelectric point of the protein. Depending on the charge of unwanted proteins, they either remain at the origin (if charges of protein and ion-exchanger are opposite) or are released from the column (if charges of protein and ion-exchanger coincide). Elution volume of the purified protein is higher than for the second group of unwanted proteins because movement of the uncharged protein of interest includes its adsorption on cellulose followed by subsequent desorption caused by the elution buffer. Problems of optimization of buffers and adsorbents are discussed. Applicability of the method of adsorption chromatography is illustrated using purification of horseradish peroxidase as an example.
Keywords: adsorption chromatography; adsorbent-ion exchanger; cellulose; buffer; peroxidase; amine

Proteome of the bacterium Mycoplasma gallisepticum by I. A. Demina; M. V. Serebryakova; V. G. Ladygina; M. A. Rogova; V. G. Zgoda; D. A. Korzhenevskyi; V. M. Govorun (165-174).
Using modern proteomic assays, we have identified the products of gene expression and posttranslational modifications of proteins of the bacterium Mycoplasma gallisepticum S6. Combinations of different technologies of protein separation by electrophoresis and mass-spectrometric analysis gave us a total of 446 proteins, i.e. 61% of the annotated proteins of this microorganism. The Pro-Q Diamond and Pro-Q Emerald dye technology was used for fluorescent detection of ten phosphoproteins and two glycoproteins. The acylation of proteins was studied by electrophoresis after in vivo labeling with different 14C-labeled fatty acids, followed by autoradiography. Sixteen acylated proteins were identified, with a quarter of them involved in plasma membrane construction and another quarter involved in cell energy metabolism.
Keywords: Mycoplasma gallisepticum ; proteomics; 2-D electrophoresis; mass spectrometry; posttranslational modifications

The interaction of human cytoplasmic phenylalanyl-tRNA synthetase (an enzyme with yet unknown 3D-structure) with homologous tRNAPhe under functional conditions was studied by footprinting based on iodine cleavage of thiophosphate-substituted tRNA transcripts. Most tRNAPhe nucleotides recognized by the enzyme in the anticodon (G34), anticodon stem (G30–C40, A31–U39), and D-loop (G20) have effectively or moderately protected phosphates. Other important specificity elements (A35 and A36) were found to form weak nonspecific contacts. The D-stem, T-arm, and acceptor stem are also among continuous contacts of the tRNAPhe backbone with the enzyme, thus suggesting the presence of additional recognition elements in these regions. The data indicate that mechanisms of interaction between phenylalanyl-tRNA synthetases and specific tRNAs are different in prokaryotes and eukaryotes.
Keywords: nucleoside-5′-O-(1-thiotriphosphate); tRNAPhe ; human phenylalanyl-tRNA synthetase; footprinting

It has been shown for 20 proteins that amino acid residues included into the protein folding nucleus, determined experimentally, are often involved in the theoretically determined amyloidogenic fragments. For 18 proteins, Φ-values indicative of the extent of residue involvement into the folding nucleus are on average higher for amino acid residues within amyloidogenic regions. Amyloidogenic fragments were predicted for 20 proteins by two methods chosen from four on the basis of comparison of prediction of amyloidogenic regions known from experimental data. Since theoretical folding nuclei are detected by the protein three-dimensional structure and amyloidogenic regions by the protein chain primary structure, the detected regularity makes possible predictions of folding nucleation sites on the basis of amino acid sequence.
Keywords: folding nucleus; amyloid fibril; globular proteins; amyloidogenic regions; FoldUnfold; Tango; Zyggregator

Conformational dynamics of human T-helper cell receptor protein CD4 has been studied with the help of monoclonal antibody (mAb) T6. The mAb T6 discriminates between s- and m-forms of CD4 and recognizes a specific conformation of the soluble (s) form of CD4 including the first nine amino acids of CD4 transmembrane sequence. However, change of tryptophan for serine in position 2 in this sequence destabilizes the T6-type conformation. By enzymatic deglycosylation and deletions of glycosylation sites, we show that T6-type conformation depends on glycosylation in both sites (Asn271 and Asn300). We show also that the sugars are not involved in direct binding to the antibody but stabilize the D3/D4 local conformation. Deglycosylated forms of sCD4 in vivo acquire a specific conformation similar to the wild type sCD4, which however cannot be restored after denaturation/renaturation under conditions of non-reducing Western blot. This observation indicates that the correct protein folding needs chaperone assistance and cannot be achieved in vitro. Completely non-glycosylated sCD4 is synthesized and secreted into the growth medium. In the medium, this mutant appears to be unstable and aggregates during time. In a contrast to soluble CD4, mutations in glycosylation sites abrogate expression of membrane CD4, thus demonstrating a different secretion pathways for soluble and membrane proteins.
Keywords: CD4; autoimmune epitope; glycosylation; protein folding; HIV-1

Theoretical structure-function analysis of all possible hemoglobin molecule fragments was performed to determine sites that could be potential sources of regulatory oligopeptides. Known data on bovine hemoglobin primary structure and information of the EROP-Moscow database concerning structure and functions of natural oligopeptides were used along with a computer program complex. A total of 6750 natural non-hemoglobin oligopeptides with hemoglobin fragments of 2–14 amino acid residues were found. Structures of 20 of them were completely identical to hemoglobin fragments. Most of the revealed oligopeptides exhibit properties of neuropeptides, antimicrobial agents, and hormones. A number of them exhibit functions previously not known for hemoglobin fragments. The possibility of natural formation of regulatory oligopeptides from hemoglobin and other food protein molecules, generation of the exogenous oligopeptide pool, their participation in regulation processes as well as accordance of results obtained here with the oligopeptide continuum concepts are discussed.
Keywords: hemoglobin; fragment; neuropeptide; antimicrobial oligopeptide; EROP-Moscow database; continuum

Extracellular chitinases of mutant superproducing strain Serratia marcescens M-1 by A. B. Duzhak; Z. I. Panfilova; T. G. Duzhak; E. A. Vasyunina (209-214).
Four extracellular proteins with chitinase activity capable of binding chitin substrates have been revealed in the culture liquid of chitinase superproducing mutant strain M-1 of Serratia marcescens. Proteins were analyzed by SDS-PAGE and MALDI-TOF mass spectrometry. Based on the data obtained, the proteins were identified as typical chitinases of S. marcescens: ChiA, ChiB, ChiC, and CBP21.
Keywords: chitinase; colloidal chitin; Serratia marcescens ; mass spectrometry

Proteomic comparative analysis of pathogenic strain 232 and avirulent strain J of Mycoplasma hyopneumoniae by Yuan-Zuo Li; Yen-Peng Ho; Shui-Tein Chen; Tzyy-Wen Chiou; Zong-Sian Li; David Shiuan (215-220).
Mycoplasma hyopneumoniae is an important pathogen of pigs causing enzootic pneumonia of swine. The pathogen remains largely enigmatic as far as the host-pathogen interactions are concerned. In the present study, the protein profiles of two strains of M. hyopneumoniae were compared by two-dimensional gel electrophoresis and mass spectrometry. The results indicate that the major adhesin P97, the 50-kDa protein derived from P159 adhesin, and the 43-kDa cleavage product of P102 are expressed at much higher levels in the pathogenic strain 232. In contrast, the avirulent strain J switches its focus to metabolism and expresses more glyceraldehyde 3-phosphate dehydrogenase in gluconeogenesis and lactate dehydrogenase, pyruvate dehydrogenase, and phosphate acetyltransferase in the pyruvate metabolism pathway. We speculate that the avirulent strain may have developed better capabilities to cope with the rich environment during repeated inoculations. Simultaneously, the capability to infect host cells may become less important so that the adhesion-related protein genes are down-regulated.
Keywords: Mycoplasma hyopneumoniae ; proteomics; virulence factors

Overexpression in Escherichia coli and purification of human fibroblast growth factor (FGF-2) by M. E. Gasparian; P. A. Elistratov; N. I. Drize; I. N. Nifontova; D. A. Dolgikh; M. P. Kirpichnikov (221-225).
Basic fibroblast growth factor (FGF-2) is a member of a large family of structurally related proteins that affect the growth, differentiation, migration, and survival of many cell types. The human FGF-2 gene (encoding residues 1–155) was synthesized by PCR from 20 oligonucleotides and cloned into plasmid pET-32a. A high expression level (1 g/liter) of a fused protein thioredoxin/FGF-2 was achieved in Escherichia coli strain BL21(DE3). The fusion protein was purified from the soluble fraction of cytoplasmic proteins on a Ni-NTA agarose column. After cleavage of the thioredoxin/FGF-2 fusion with recombinant human enteropeptidase light chain, the target protein FGF-2 was purified on a heparin-Sepharose column. The yield of FGF-2 without N- and C-terminal tags and with high activity was 100 mg per liter of cell culture. Mutations C78S and C96S in the amino acid sequence of the protein decreased FGF-2 dimer formation without affecting its solubility and biological activity.
Keywords: growth factors; FGF-2; recombinant proteins; E. coli

Novel trypsin inhibitors from the white rot fungus Abortiporus biennis were isolated, partially purified, and char- acterized. The inhibitors were purified by heat treatment, anion-exchange chromatography, and gel filtration. SDS-PAGE of the purified preparation demonstrated the presence of two proteins with molecular masses of 20 and 21.5 kDa. The A. biennis inhibitors were most active against trypsin, while chymotrypsin α, proteinase K, and Carlsberg subtilisin were inhibited to a smaller extent. The inhibitors are acidic proteins with remarkably high heat stability.
Keywords: Abortiporus biennis ; protease inhibitors; white rot fungi; Basidiomycetes

Protein aggregation and neurodegeneration: Clues from a yeast model of Huntington’s disease by N. Bocharova; R. Chave-Cox; S. Sokolov; D. Knorre; F. Severin (231-234).
A number of neurodegenerative diseases are accompanied by the appearance of intracellular protein aggregates. Huntington’s disease (HD) is caused by a mutation in a gene encoding huntingtin. The mutation causes the expansion of the polyglutamine (polyQ) domain and consequently polyQ-containing aggregates accumulate and neurons in the striatum die. The role of the aggregates is still not clear: they may be the cause of cytotoxicity or a manifestation of the cellular attempt to remove the misfolded proteins. There is accumulating evidence that the main cause of HD is the interaction of the mutated huntingtin with other polyQ-containing proteins and molecular chaperones and most studies based on a yeast model of HD support this point of view. Data obtained using yeasts suggest pathological consequences of polyQ-proteasomal interaction: proteasomal overload by polyQs may interfere with functions of the cell cycle-regulating proteins.
Keywords: Huntington’s disease; aggregation; polyglutamine; yeast