[Structure and evolutionary role of the Penelope mobile element in Drosophila species of the virilis group]. / Struktura i évoliutsionnaia rol' mobil'nogo élementa Penelopa u vidov Drosophila gruppy virilis.

The mobile element Penelope is activated and mobilizes several other transposons in dysgenic crosses in Drosophila virilis. Its structure proved to be complex and to vary greatly in all examined species of the virilis group. Phylogenetic analysis of the reverse transcriptase (RT) domain assigned Penelope to a new branch, rather than to any known family, of LTR-lacking retroelements. Amino acid sequence analysis showed that the C-terminal domain of the Penelope polyprotein is an active endonuclease, which is related to intron-encoded endonucleases and to bacterial repair endonuclease UrvC, and may act as an integras. Retroelements coding for a putative endonuclease that differs from typical integrase have thus far not been known. The N-terminal domain of the Penelope polyprotein was shown to contain a protease with significant homology to HIV-1 protease. Phylogenetic analysis divided the Penelope copies from several virilis species into two subfamilies, one including virtually identical full-length copies, and the other comprising highly divergent defective copies. The results suggest both vertical and horizontal transfer of the element. Possibly, Penelope invasion recurred during evolution and contributed to genome rearrangement in the virilis species. Chromosome aberrations detected in D. virilis, which is now being invaded by Penelope, is direct evidence for this assumption.

[Amino acid sequence analysis of barley stripe mosaic viral proteins: tentative identification of viral serine proteases]. / Analiz aminokislotnykh posledovatel'nostei belkov virusa shtrikhovatoi mozaiki iachmenia: predpolozhitel'naia identifikatsiia virusnoi serinovoi proteazy.

Analysis of amino acid sequences of barley stripe mosaic virus (BSMV) proteins revealed the pentapeptide GDSGG, the sequence unique for catalytic centers of serine chymotrypsin-like proteases, in protein p14 encoded by open reading frame 4 of RNA beta. Computer-assisted comparisons revealed a statistically significant similarity between amino acid sequences of p14 and chymotrypsin-like proteases. The catalytic His and Asp residues tentatively identified in p14 together with the Ser residue of the GDSGG sequence, presumably, constitute the "catalytic triad" characteristic of chymotrypsin-like proteases. Based on these observations and on the presence of a potential N-proximal transmembrane domain in p14, this protein may be suggested to be a serine protease involved in processing of the replicase precursor within a membrane-bound replication complex of BSMV.

[Evolution of RNA-dependent RNA-polymerases from positive RNA viruses: comparison of phylogenetic trees constructed by different methods]. / Evoliutsiia RNK-zavisimykh RNK-polimeraz pozitivnykh ribovirusov: sravnenie filogeneticheskikh derev'ev, postroennykh raznymi metodami.

Presumptive phylogenetic trees of evolutionary conserved fragments of RNA-dependent RNA polymerases of 26 positive strand RNA viruses were generated using a simple clustering procedure or a novel approach based on the so-called maximal topologic similarity principle. The latter methodology involves a quantitative measure of the degree of correspondence between the topology of generated trees and structure of the initial distance matrix. The algorithm for tree construction based on the maximal topologic similarity principle does not include the assumption of evolutionary rate constancy, as opposed to the clustering procedure. Nevertheless, it is demonstrated that the trees generated by the two methods are topologically similar, indicating that no drastic change of evolutionary rate had occurred in evolution of the positive strand RNA virus RNA polymerases. This in turn suggests that RNA-dependent RNA polymerases (or at least their evolutionary conserved core domains used for construction of the phylogenetic trees) are principally functionally equivalent in all positive strand RNA viruses.

[Bacteriophage Mu transposase contains a fragment with primary structure similar to that of protein VPg covalently linked with poliovirus RNA]. / Prisutstvie v transpozaze bakteriofaga Mu fragmenta, skhodnogo po pervichnoi strukture s belkom VPg, kovalentno sviazannykh s RNK poliovirusa.

A statistically valid similarity was found to exist between the amino acid sequences of poliovirus genome-linked protein VPg and a fragment of bacteriophage Mu transposase (Mu A protein). Based on this observation a hypothesis is proposed that the molecular mechanisms underlying the functions of the two proteins may be analogous. Both proteins are supposed to be site-specific endonucleases which form covalent linkage with the 5'-phosphate group of the nicked DNA or RNA strand. The amino acid residue participating in the formation of this linkage in MuA is tentatively identified as Tyr413.

[Evolution of RNA-dependent RNA polymerases of positive riboviruses]. / Evoliutsiia RNK-zavisimykh RNK-polimeraz pozitivnykh ribovirusov.

A comparative analysis is presented of 24 known amino acid sequences of RNA-dependent RNA polymerases of positive strand RNA viruses infecting animals, plants and bacteria. Using a newly proposed methodology of group alignment for weakly similar sequences, evolutionary conserved fragments of all these proteins were unambiguously aligned. A unique pattern (consensus) of 7 invariant amino acid residues was revealed which is absent from the sequences of other RNA and DNA polymerases and is thought to unequivocally identify the RNA-dependent RNA polymerases of positive strand RNA viruses. Based on the obtained alignment a tentative phylogenetic tree of viral RNA polymerases was constructed for the first time. The RNA-dependent RNA polymerases of positive strand RNA viruses are concluded to comprise a distinct family of evolutionary related proteins.

[Prediction of the nucleotide-binding properties of viral proteins from their primary structure]. / Predskazanie nukleotidsviazyvaiushchikh svoistv virusnykh belkov po ikh pervichnoi strukture.

Screening of amino acid sequences of a variety of virus-specific proteins for fragments structurally similar to the "ATP-consensus", a universal sequence found in nucleotide-binding pockets of several ATP-utilizing enzymes, was made. Fragments of hypothetical nucleotide-binding pockets were discovered in some proteins of DNA viruses (herpesviruses, papovaviruses, poxviruses and parvoviruses, comoviruses, bromoviruses, alpha 1-phaviruses and tobamoviruses). Analysis of the published data concerning the functions of the virus-specific proteins in question makes it evident that the proposal that these proteins possess nucleotide-binding properties. Is confirmed by these data or, at least does, not contradict to them. The possibility of a common evolutionary origin of the proteins containing fragments similar to the "ATP-consensus" is discussed.