PubMed Health⌕ Search

Biomedical subjects

P V Sergiev

Publications and source records attributed to P V Sergiev.

13 recordsLinked to original sources
PubMed2006

Does a deficiency of the signal recognition particle (SRP)-pathway affect the biosynthesis of its components in Saccharomyces cerevisiae and Escherichia coli?

We studied the behavior of the signal recognition particle (SRP) components in Saccharomyces cerevisiae upon deficiencies of the protein transport caused by the absence of the SRP membrane receptor alpha-subunit. A decrease in the concentration of the SRP membrane receptor alpha-subunit in the cell significantly decreased the level of an SRP component, protein SRP72, as well as the levels of mRNAs of SRP protein components and the SRP receptor beta-subunit. But the amount of 7SL RNA remained unchanged. In contrast, in Escherichia coli cells the gradual decrease in the level of the protein FtsY (a homolog of the SRP membrane receptor alpha-subunit) was not associated with changes in the Ffh protein level.

Escherichia coli↗
PubMed2001

A protonated base pair participating in rRNA tertiary structural interactions.

In the recently published X-ray crystallographic structure for the 50S subunit of Haloarcula marismortui ribosomes, residue U2546 of the 23S rRNA forms a non-Watson-Crick base pair with U2610. The corresponding residues in the secondary structure of the Escherichia coli 23S molecule are U2511 and C2575, and it follows that the latter base (C2575) should be protonated in order to form a base pair that is isostructural with its counterpart in H.marismortui. This prediction was demonstrated experimentally by reduction with sodium borohydride followed by primer extension analysis; borohydride is able to reduce positively charged bases, yielding products which block reverse transcription. In the course of the analysis a further charged base pair (AH(+)1528-G1543) was identified in the E.coli 23S molecule. Both charged pairs (U2511-CH(+)2575 and AH(+)1528-G1543) were only observed in the context of the intact ribosomal subunit and were not seen in deproteinized rRNA.

Base Pairing↗
PubMed2001

Saturation mutagenesis of 5S rRNA in Saccharomyces cerevisiae.

rRNAs are the central players in the reactions catalyzed by ribosomes, and the individual rRNAs are actively involved in different ribosome functions. Our previous demonstration that yeast 5S rRNA mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. At the time, however, the highly repetitive nature of the genes encoding rRNAs precluded more detailed genetic and molecular analyses. A new genetic system allows all 5S rRNAs in the cell to be transcribed from a small, easily manipulated plasmid. The system is also amenable for the study of the other rRNAs, and provides an ideal genetic platform for detailed structural and functional studies. Saturation mutagenesis reveals regions of 5S rRNA that are required for cell viability, translational accuracy, and virus propagation. Unexpectedly, very few lethal alleles were identified, demonstrating the resilience of this molecule. Superimposition of genetic phenotypes on a physical map of 5S rRNA reveals the existence of phenotypic clusters of mutants, suggesting that specific regions of 5S rRNA are important for specific functions. Mapping these mutants onto the Haloarcula marismortui large subunit reveals that these clusters occur at important points of physical interaction between 5S rRNA and the different functional centers of the ribosome. Our analyses lead us to propose that one of the major functions of 5S rRNA may be to enhance translational fidelity by acting as a physical transducer of information between all of the different functional centers of the ribosome.

Alleles↗
PubMed2000

Mutations at position A960 of E. coli 23 S ribosomal RNA influence the structure of 5 S ribosomal RNA and the peptidyltransferase region of 23 S ribosomal RNA.

The proximity of loop D of 5 S rRNA to two regions of 23 S rRNA, domain II involved in translocation and domain V involved in peptide bond formation, is known from previous cross-linking experiments. Here, we have used site-directed mutagenesis and chemical probing to further define these contacts and possible sites of communication between 5 S and 23 S rRNA. Three different mutants were constructed at position A960, a highly conserved nucleotide in domain II previously crosslinked to 5 S rRNA, and the mutant rRNAs were expressed from plasmids as homogeneous populations of ribosomes in Escherichia coli deficient in all seven chromosomal copies of the rRNA operon. Mutations A960U, A960G and, particularly, A960C caused structural rearrangements in the loop D of 5 S rRNA and in the peptidyltransferase region of domain V, as well as in the 960 loop itself. These observations support the proposal that loop D of 5 S rRNA participates in signal transmission between the ribosome centers responsible for peptide bond formation and translocation.

Aldehydes↗
PubMed1998

The Database of Ribosomal Cross links (DRC).

The Database of Ribosomal Cross-links (DRC) provides a complete collection of all the published data produced by cross-linking studies on the Escherichia coli ribosome, as well as on its components and functional ligands. The DRC currently includes data on 986 cross-links from >100 research papers, yielded by >40 different reagents. For each cross-link, information is given concerning its location in the ribosome, the chemical or photochemical reagent applied, a brief description of the method(s) used to locate the cross-link, and the literature reference. The DRC is freely available via the World Wide Web at: http://Ribosome.Genebee.MSU.SU/DRC/ or at http://WWW:MPIMG-Berlin-Dahlem.MPG.DE/[symbol: see text]baranov/DRC/

Computer Communication Networks↗
PubMed1998

Structure of the decoding center of the ribosome.

The decoding center of the ribosome provides mRNA translation and the fidelity of the codon--anticodon interactions along with mRNA translocation in the course of protein biosynthesis. The three-dimensional structure of the ribosome decoding center is still unknown. However, up to now a number of direct and indirect experimental data on the structural and functional organization of the decoding center have been obtained. In this paper the main components of the decoding center are described on the basis of our own experimental results combined with data from the literature. A model of their spatial arrangement at the small ribosomal subunit is suggested.

Base Sequence↗
PubMed1997

The path of mRNA through the bacterial ribosome: a site-directed crosslinking study using new photoreactive derivatives of guanosine and uridine.

Two new photoreactive nucleotide derivatives have been applied in site-directed crosslinking studies with mRNA analogues. 6-Thioguanosine triphosphate or 5-methyleneaminouridine triphosphate was incorporated into mRNA analogues by T7 transcription; after transcription, the 5-methyleneaminouridine residues were converted to a diazirine derivative. mRNA analogues carrying either 6-thioguanosine or the diazirine derivative were bound to Escherichia coli ribosomes in the presence of tRNA(f)(Met), and photo-crosslinking was induced by irradiation at 350 nm. With 6-thioguanosine, specific crosslinks were observed from downstream positions +8 or +9 of the mRNA to nt 1196 in helix 34 of the 16S rRNA, and from position +12 to nt 530 in helix 18. With the diazirine derivative, a crosslink from position +2 (within the AUG codon) to nt 926 in helix 28 was found. Taken together with previous data obtained from downstream sites in mRNA analogues carrying 4-thiouridine residues, specific crosslinks have now been identified from downstream mRNA positions +2, +4, +6, +7, +8, +9, +11, and +12. The data confirm that the three 16S rRNA regions involved-helices 18, 28, and 34-are in the direct neighborhood of the decoding area of the 30S subunit.

Bacteriophage T7↗
PubMedDate not supplied

[Study of ribosome structure using the biochemical methods: judgment day].

The data on RNA-RNA interactions between the components of the E. coli translation machinery obtained by X-ray crystallography and chemical methods are compared. The approaches to the study of RNA secondary and tertiary structure are assessed. The following conclusions are made: comparative sequence analysis and compensatory mutations approach both give reliable data on the RNA secondary structure. The chemical modification technique provides good results. Local cleavage of internucleotide bonds by hydroxyl radicals is reliable in the frame of its 40 A resolution, in contrast to the application of copper-phenanthroline complex as a cleavage reagent, which is unreliable. Direct UV irradiation and nitrogen mustard treatment are the best methods of crosslink generation. In vitro transcription is the only good method for the incorporation of nucleotide analogs in RNA. RNase H hydrolysis and/or nucleotide-specific RNases fingerprints must be applied for the crosslink site determination in parallel with reverse transcription.

Base Sequence↗
PubMedDate not supplied

[Escherichia coli ribosomes as the model to test new photoactivated tRNA analogues, containing 6-thioguanosine].

Photoreactive derivatives of tRNAs, containing 6-thioguanosine or diazirine derivative of 5-methyleneaminouridine were compared as probes to modify Escherichia coli ribosomes. The derivatives of tRNA were synthesized by T7 transcription Proportion of the modified nucleotide analogues was optimised to obtain good yield, analogue incorporation and binding to the ribosome. Complexes of the tRNA analogues with the ribosomal P-site were irradiated with mild UV light. Cross-links were analysed by oligonucleotide-directed hydrolysis of rRNA by RNase H and reverse transcription. 6-thioguanosine was proved to be a perspective reagent for cross-linking studies of complex ribonucleoproteides.

Cross-Linking Reagents↗
PubMedDate not supplied

[GTPases of translational apparatus].

Protein biosynthesis is a complex biochemical process. It integrates multiple steps where different translation factors specifically interact with the ribosome in a precisely defined order. Among the translation factors one can find multiple GTP-binding or G-proteins. Their functioning is accompanied by GTP hydrolysis to the GDP and inorganic phosphate ion Pi. Ribosome stimulates the GTPase activity of the translation factors, thus playing a role analogues to GTPase-activating proteins (GAP). Translation factors--GTPases interact with the ribosome at all stages of protein biosynthesis. Initiation factor 2 (IF2) catalyse initiator tRNA binding to the ribosomal P-site and subsequent subunit joining. Elongation factor Tu (EF-Tu) is responsible for the aminoacyl-tRNA binding to the ribosomal A-site, while elongation factor G (EF-G) catalyses translocation of mRNA in the ribosome by one codon, accompanied by tRNA movement between the binding sites. In its turn, release factor 3 (RF3) catalyse dissociation of the ribosomal complex with release factors 1 or 2 (RF1 or RF2) following the peptide release. This review is devoted to the functional peculiarities of translational GTPases as related to other G-proteins. Particularly, to the putative GTPase activation mechanism, structure and functional cycles.

Enzyme Activation↗
PubMedDate not supplied

[The structural changes in the ribosome during the elongation cycle].

The plenty of data about structural changes in the ribosome during its functioning has been accumulated. The most interesting information on such changes was obtained by cryo-EM of various ribosomal complexes with the ligands and by combination of rRNA site-directed mutagenesis with the analysis of structural changes in ribosome by chemical modification technique (chemical probing). The most studied structural transformations of the ribosome interacting with tRNAs and elongation factors are considered in this review. The structural rearrangements are discussed in the context of interactions between the functional centers of the ribosome. We also describe the system of tertiary contacts between the rRNA helices and proteins which forms the universal structure in the ribosome. We pay attention that by means of such system the allosteric conformational signal can be transmitted between the functional centers. Besides the discussion of different biochemical data in the scope of structural data we also consider the hypothesis that the position of GTPase associated center (GAC) in the ribosome regulates the binding of elongation factors.

Cryoelectron Microscopy↗