[Species diversity of deep water microorganisms in Lake Baikal, detected by 16S rRNA sequences].
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Bacteria↗
Biomedical subjects
M A Grachev
Publications and source records attributed to M A Grachev.
Comparative study of two protein-coding regions of mitochondrial DNA from three endemic sculpins (Cottoidei) of Lake Baikal.
Two protein-coding regions (cytochrome b, ATPase 8, and part of ATPase 6) from mitochondrial DNA of Cottus kessleri, Cottocomephorus grewingki, and Cottocomephorus inermis--Baikalian endemic sculpins--were amplified via polymerase chain reaction, and sequenced. Two novel primers--L8352 (5'-TAAAGATTGGTGAC TCCCAACCACC) and H8773 (5'-GTAGGGAGT AAGCCCAATATGTT)--were used for the latter region. Phylogenies suggested by sequence divergence of the genes of ATPases appeared to be different from those computed from data for cytochrome b. The time of species branching was estimated as 1-2 million years (Myr) on the basis of merged sequences. Hence, members of the Baikalian cottoid species flock are much more distant from each other than members of the cichlid fish flocks of the great lakes of Africa (0.2 Myr). Topology of the phylogenetic tree does not contradict the relationships derived from morphological data. However, genetic distances suggest that C. grewingki and C. inermis are not sister species, contrary to general belief.
Adenosine Triphosphatases↗
[Amino acid sequence of myoglobin from seals from Lake Baikal].
The primary structure of myoglobin of the seal of Lake Baikal (East Siberia) Phoca siberica, determined by sequencing the whole protein and peptides obtained by the cyanogen bromide or proteinase cleavage and separated by the microcolumn liquid chromatography, was found to be identical to the primary structures of myoglobins of the harbour seal Phoca vitulina largha and the grey seal Halehoerus gryphus. It suggests that these species separated from a common ancestor less than seven million years ago.
Amino Acid Sequence↗
Mapping the active site of yeast RNA polymerase B (II).
Yeast RNA polymerase B (II) was incubated with a collection of 13 different nucleotide derivatives and affinity labeled by allowing DNA-directed phosphodiester bond formation. The 32P-labeled site was localized in the C-terminal part of the B150 subunit by microsequencing a proteolytic fragment, then further mapped by a combination of extensive or single-hit chemical cleavage reactions and analysis of the labeled peptide patterns. The affinity label was mapped to between Asn946 and Met999, within one of the nine regions that are conserved between B150 and the bacterial beta subunit. The results underscore the conservative evolution of the catalytic center of eukaryotic and bacterial RNA polymerases.
Amino Acid Sequence↗
Localisation of the binding site for the initiating substrate on the RNA polymerase from Sulfolobus acidocaldarius.
RNA polymerase from the archaebacterium Sulfolobus acidocaldarius was chemically modified with AMP o-formylphenyl ester followed by reduction with borohydride. The modified protein catalyzes the labeling of its own largest subunit when incubated with [alpha-33P]UTP in the presence of poly[d(A-T)]. On cleaving of the labeled protein using cyanogen bromide, hydroxylamine or amino acid-specific endoproteinases for a very brief period, the pattern and size of the radioactive fragments formed are best explained by attachment of the label between Gly843 and Met895 of the largest subunit. In this region there exists a highly conserved sequence which is also found in other archaebacterial, eukaryotic and prokaryotic RNA polymerase. This suggests that the binding site for the initiating substrate of RNA polymerases has been conserved during evolution.
Affinity Labels↗
Studies of the functional topography of Escherichia coli RNA polymerase. A method for localization of the sites of affinity labelling.
A method is proposed for localization of the sites of affinity labelling of the beta subunit of Escherichia coli RNA polymerase. The principle of this method is similar to that of the methods of rapid sequencing of nucleic acids. The polypeptide bearing a radioactive affinity label at one of the amino acid residues is subjected to short-term treatment with cyanogen bromide. The conditions of this reaction are selected in such a way that less than one cleavage occurs on average per polypeptide chain. Two series of radioactive peptides are formed, one involving all the possible N-terminal peptides and the other the C-terminal peptides. The distribution of the lengths of these peptides is studied by means of gel electrophoresis and compared with the theoretical ones based on the known amino acid sequence of the beta subunit. Obviously, the affinity label resides between the C-terminus of the shortest N-terminal radioactive peptide and the N-terminus of the shortest C-terminal radioactive peptide. In order to increase reliability and resolution of the method, partial trypsinolysis may be employed. The evidence obtained suggests that lysine residues over the regions 1036-1066, 1234-1242, and histidine-1237 are situated in the nearest neighbourhood to, or directly involved in the formation of the active center of initiating substrate binding of the beta subunit of E. coli RNA polymerase.
Affinity Labels↗
[Accumulation of chlorophenols in fishes in wood-pulp industry waste waters].
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Animals↗
Determination and characterization of chloroguaiacol conjugates in fish bile by HPLC.
In this study a small-scale technique for direct analysis of metabolic conjugates of 4,5,6-trichloro- (CG-3) and tetrachloroguaiacols (CG-4) in fish bile by RP-HPLC is presented. Only one metabolite, glucuronic acid conjugate, was demonstrated in two Lake Baikal fishes (Leuciscus leuciscus baikalensis and Cottus kessleri) exposed to CG-3 or CG-4 at 6 degrees C for 1-2 days. In Leuciscus the ratio between free CG-4 in the ambient water and conjugated CG-4 in the bile averaged 264,000. Intraperitoneal injections of tetrachloroveratrol (CV-4) into Thymallus arcticus baikalensis did not reveal any traces of free CV-4 or CG-4 glucuronide in the bile in 2 days at 5 degrees C. We therefore suggest that CV-4 was not demethylated and subsequently conjugated with glucuronic acid in the liver of this fish species.
Journal Article↗
[Immune electron microscope localization of RNA-polymerase on the Escherichia coli chromosome using monoclonal antibodies against the beta-subunit].
Possibility of the immunoelectron microscopic visualization of RNA polymerase on the Escherichia coli chromosome with monoclonal antibodies against the beta-subunit labelled by [protein A.gold] complex was demonstrated. Using this method RNA polymerase molecules were revealed within nucleoid as well as on the membrane-free chromosome.
Antibodies, Monoclonal↗
Active site labeling of the RNA polymerases A, B, and C from yeast.
RNA polymerases A, B, and C from yeast were modified by reaction with 4-formylphenyl-gamma-ester of ATP as priming nucleotide followed by reduction with NaBH4. Upon phosphodiester bond formation with [alpha-32P]UTP, only the second largest subunit, A135, B150, or C128, was labeled in a template-dependent reaction. This indicates that these polypeptide chains are functionally homologous. The product covalently bound to B150 subunit was found to consist of a mixture of ApU and a trinucleotide. Enzyme labeling exhibited the characteristic alpha-amanitin sensitivity reported for A and B RNA polymerases. Labeling of both large subunits of enzyme A and B but not of any of the smaller subunits was observed when the reduction step stabilizing the binding of the priming nucleotide was carried out after limited chain elongation. These results illustrate the conservative evolution of the active site of eukaryotic RNA polymerases.
Adenosine Triphosphate↗
Studies of the functional topography of Escherichia coli RNA polymerase. Affinity labelling of RNA polymerase in a promoter complex by phosphorylating derivatives of primer oligonucleotides.
Amidation of the 5'-phosphate group of the heptanucleotide pdApdApdApdTpdCpdGprC and of its derivatives of the general formula (pdN)npdGprC (n = 0-5) with imidazole, N-methylimidazole, and 4-dimethylaminopyridine afforded a series of phosphorylating affinity reagents. The parent oligonucleotides of this series complementary to promoter A2 of T7 phage over the region (-5 to +2) are known to be efficient primers of the synthesis of RNA by Escherichia coli RNA polymerase with promoter A2 as template. Treatment of the complex RNA-polymerase X promoter-A2 with affinity reagents followed by addition of [alpha-32P]UTP resulted in labelling of RNA polymerase by the residues -(pdN)npdGprCprU (p = radioactive phosphate). This affinity labelling was highly selective because elongation of the covalently bound residues (pdN)npdGprC by prU residues was catalyzed by the active center of RNA polymerase. The most efficient reagents were N-methylimidazolides. A dramatic change of the pattern of labelling of the subunits beta, beta', and sigma took place with changing n. Maximum labelling of the beta subunit occurred at n = 1 and of the sigma subunit at n = 5. The targets in both the subunits were His residues. The alpha subunit was not specifically labelled.
Affinity Labels↗
Studies on the functional topography of Escherichia coli RNA polymerase. Highly selective affinity labelling by analogues of initiating substrates.
RNA polymerase was treated in the presence of promoter-containing templates with 16 affinity reagents, derivatives on NMPs, NDPs and NTPs with reactive substituents at the terminal phosphate. This treatment was followed by addition of a pyrimidine [alpha-32P]NTP. Due to 'catalytic competence' of some of the residues of the affinity reagents bound covalently near the active center at the first stage, active-center-catalyzed synthesis of a phosphodiester bond occurred, and radioactive residues with the general formula -pNpN (where p = radioactive phosphate) appeared covalently attached to the enzyme. Such affinity labelling was super-selective because affinity reagent residues bound outside the active center were not elongated and thus remained non-radioactive. Labelling took place only when the combination of the reagent and [alpha-32P]NTP corresponded to the sequence of nucleotides of the promoter. With reagents having short 'arms', only the beta subunit was labelled; the targets were His and/or Lys residues. With reagents having longer 'arms', the sigma subunit was also labelled.
Affinity Labels↗
[Localization of lysine residues in the site of initiating substrate binding of E. coli RNA-polymerase].
Superselective affinity labelling of E. coli RNA polymerase in a complex with the promoter-containing fragment of T7 DNA by treatment with orto-formylphenyl ester of GMP followed by addition of [alpha-33P]UTP resulted in covalent binding of the residue--pGpU (p-radioactive phosphate) with one of lysine residues of the beta-subunit, Lys1048, Lys1051, Lys1057, Lys1065. The amino acid sequence of this region of the beta-subunit of E. coli RNA polymerase has a high extent of homology with that deduced for a region of tobacco chloroplast RNA polymerase on the basis of the nucleotide sequence of the chloroplast rpoB-like gene.
Affinity Labels↗
[Highly selective affinity labeling of a promoter in a complex with E. coli RNA-polymerase by alkylating derivatives of initiating substrates].
The complex [promoter A2 X E. coli RNA polymerase] was treated with phosphoamides, derivatives of 4-[N-methyl, N-(2-chloroethyl)]-aminobenzylamine and guanosine-5'-mono-, di-, and triphosphates with the alkylating group attached to the terminal phosphates. After this, [alpha-32P]CTP was added. Residues of the affinity reagents bound covalently at the first stage were elongated by radioactive -pC residues due to the catalytic action of the active centre of RNA polymerase. Affinity labelled were beta-and sigma-subunits of the enzyme, and the promoter. The affinity label was localized on -pGpC residues. A guanine residue was alkylated in the promoter as suggested by radioactivity elimination kinetics. As the data obtained and the previously known length of the reagent (maximum distance between the alpha-phosphorus atom of the reagent and the point of alkylation is less than 0.6 nm) indicate, there is a direct rather than protein-mediated contact between the template and the substrate within the complex [promoter X RNA polymerase].
Affinity Labels↗
[Localization of a histidine residue in the binding site for the initiating substrate of E. coli RNA-polymerase].
E. coli RNA polymerase was selectively labelled in the presence of promoters at a histidine residue of the beta-subunit by treatment with GDP beta-imidazolide and then with [alpha-32P]UTP (or [alpha-33P]UTP). Partial cyanogen bromide cleavage of the labelled polypeptide afforded a series of "single-hit" labelled peptides, the electrophoretic pattern of which suggested that the labelling site was His1237. This conclusion was confirmed by a similar pattern obtained with products of the cyanogen bromide cleavage of a radioactive peptide obtained by the limited trypsinolysis (C-terminal peptide consisting of 423 amino acid residues). Interpretation of our earlier results in favour of His1116 as the labelling point (Dokl. Acad. nauk SSSR, 1985, v. 281, p. 723) was incorrect due to the electrophoretic "compression" of three labelled peptide bands.
Amino Acid Sequence↗
[Highly selective affinity labeling of DNA-dependent RNA-polymerase of bacteriophage T7].
T7 phage RNA polymerase was affinity labelled in the presence of its promoter by treatment with an ATP gamma-derivative (a phosphoamide obtained from 4-(N-chloroethyl, N-methyl)aminobenzylamine, or one of esters obtained from 2-methoxy-4-formylphenol, 4-formylphenol, and 2[N-(4-formylphenyl), N-methyl]-aminoethanol) followed by addition of [alpha-32P]GTP. The most efficient labelling took place with the alkylating phosphoamide reagent.
Affinity Labels↗
[Addressed modification of the promoter region of DNA in a complex with RNA polymerase by alkylating oligonucleotide derivatives].
Addressed chemical modification of double-stranded DNA unwound with the specific protein has been demonstrated. 4(N-2-chloroethyl-N-methylamino)benzyl-5'-phosphoamides of oligonucleotides d(CG)rC, d(ATCG)rC, d(AATCG)rC, which can serve as primers in the RNA polymerase-catalyzed transcription, alkylated A2 promoter region of pSK-A2 plasmid in its "open" complex with E. coli RNA polymerase.
Alkylating Agents↗