[Correlation of the width of annual tree rings with climatic changes and solar activity]. / Issledovanie korrreliatsii shiriny godichnykh kolets derev'ev s klimaticheskimi izmeneniiami i solnechnoi aktivnost'iu.

Fluctuations in the width of annual tree rings in the time interval from the eighth century till the present time were analyzed on the basis of dendroclimatic scales. Periods of extremely high and low growth of trees were distinguished, and their correlations with heliogeophysical factors were studied. The major climatic parameters determining the growth of trees are warmth and moisture; a small gain is observed in cold and droughty periods. No correlations between the width of tree rings and the minima and maxima of solar activity cycles were observed with the method used.

In situ measurements of optical parameters in Lake Baikal with the help of a Neutrino telescope.

We present results of an experiment performed in Lake Baikal at a depth of approximately 1 km. The photomultipliers of an underwater neutrino telescope under construction at this site were illuminated by a distant laser. The experiment not only provided a useful cross-check of the time calibration of the detector but also allowed us to determine inherent optical parameters of the water in a way that was complementary to standard methods. In 1997 we measured an absorption length of 22 m and an asymptotic attenuation length of 18 m. The effective scattering length was measured as 480 m. By use of (cos theta) = 0.95 (0.90) for the average scattering angle, this length corresponds to a geometric scattering length of 24 (48) m.

Expression of the turnip yellow mosaic virus proteinase in Escherichia coli and determination of the cleavage site within the 206 kDa protein.

The large non-structural polyprotein (206 kDa) of turnip yellow mosaic tymovirus (TYMV) undergoes auto-cleavage, producing N- and C-terminal proteins. Here we show that the viral proteinase responsible for this event is active when produced in Escherichia coli, as monitored in Western blots by examining the generation of the C-terminal cleavage product after induction by IPTG. The outer boundaries and critical amino acids of the proteinase domain were characterized by deletion analysis and site-directed mutagenesis. A miniproteinase of 273 residues resulting from combined N- and C-terminal deletions still performed efficient cleavage. Sequence analysis of the bacterially-purified C-terminal cleavage product indicated that cleavage occurs between Ala1259 and Thr1260 of the non-structural protein.

Complete sequence of an infectious full-length cDNA clone of citrus tatter leaf capillovirus: comparative sequence analysis of capillovirus genomes.

The complete nucleotide sequence of citrus tatter leaf capillovirus (CTLV lily strain) was determined. It is 6496 nucleotides long, excluding the 3'-terminal poly(A) tract, and contains two putative overlapping open reading frames (ORFs). ORF1 (positions 37-6354) encodes a potential polyprotein of molecular mass 242 kDa. ORF2 (positions 4788-5750) codes for a 36 kDa protein. The 242 kDa polypeptide contains several non-structural protein domains (i.e. methyltransferase, NTP-binding helicase, papain-like proteinase and polymerase) and, at its C terminus, the putative coat protein. The N-terminal region of the 36 kDa protein displays sequence similarity to the cell-to-cell movement proteins of the '30 K superfamily'. Such a genome structure is conserved between CTLV and apple stem grooving capillovirus. Capped transcripts from a plasmid containing the complete sequence of CTLV, with a T7 RNA promoter, successfully infected Chenopodium quinoa plants and caused symptoms characteristic of CTLV. Uncapped transcripts were noninfectious.

Autocatalytic processing of the 223-kDa protein of blueberry scorch carlavirus by a papain-like proteinase.

The first open reading frame of the blueberry scorch carlavirus (BBScV) genome encodes a putative replication-associated protein of 223 kDa (p223). A pulse-chase analysis of viral RNA translated in vitro in rabbit reticulocyte lysate revealed that p223 was proteolytically processed. Using a full-length ORF 1 cDNA clone in a coupled in vitro transcription/translation reaction, we confirmed that the ORF 1 gene product of BBScV processes autocatalytically. From sequence alignments with phylogenetically related viruses, including tymoviruses, we predicted that p223 contained a papain-like proteinase domain with a putative catalytic cysteine994 and histidine1075. A second possible proteinase domain, which contained cysteine895 and histidine984 residues with similar spacing but was otherwise less similar to the viral papain-like proteinases, was identified immediately upstream of the predicted catalytic site. The cleavage site of the proteinase was predicted to be between the putative helicase and the polymerase domains, possibly between or close to glycine1472 and alanine1473. Supporting these predictions, deletion of the 2091 nucleotides encoding the C-terminal region of p223, which contained the putative RNA polymerase domain and the putative cleavage site of the polyprotein, abolished autoproteolysis. Deletion of the 2061 nucleotides encoding the N-terminal region, which contained the putative methyltransferase domain, did not affect autoproteolysis. Alteration of cysteine994, histidine1075, or glycine1472 abolished autoproteolysis in vitro, supporting the involvement of these residues at the catalytic site and cleavage site. Alteration of the upstream cysteine895 and histidine984 residues did not affect processing in vitro. Capped BBScV full-length transcripts containing mutations in the codons for either cysteine994 or histidine1075 were not infectious in the systemic host plants Chenopodium quinoa and C. amaranticolor, whereas alteration of glycine1472 signficantly decreased but did not abolish infectivity. Transcripts containing mutations in the codons for either cysteine895 or histidine984 also were infectious, but resulted in delayed symptom expression in plants.

Papain-like proteinase of turnip yellow mosaic virus: a prototype of a new viral proteinase group.

Sequence comparisons predicted a potential papain-like proteinase domain in the N-terminal cleavage product (NRP) of the large nonstructural replicase polyprotein (RP) of turnip yellow mosaic virus (TYMV). Replacement of the predicted catalytic amino acids, Cys-783 by Ser, or of His-869 by Glu, abolished cleavage of the 206K RP into a approximately 150 K NRP and a approximately 78 K C-terminal product in reticulocyte lysates, while other substitutions exerted no apparent influence on proteolysis. The proteinase-deficient mutant RPs could not be cleaved in trans by as much as an eight-fold molar excess of wild-type proteinase. Deletion experiments have excluded the possible influence on autoproteolysis of amino acid sequences 1-708 and 982-1204 flanking the proteinase domain. Thus, the proteinase of TYMV with a papain-like dyad of essential amino acids has been mapped just upstream from the putative NTPase domain. Statistically significant sequence similarities with the TYMV proteinase were found for the similarly located domains of the replicase polyproteins of carlaviruses, capilloviruses, apple stem pitting virus and apple chlorotic leaf spot virus as well as for those of other tymoviruses and for the domain located downstream from the putative NTPase domain of the large polyprotein of beet necrotic yellow vein furovirus. All these domains are not significantly similar to other known proteinases, although they conserve papain-like Cys- and His-containing motifs. Thus these domains constitute a compact group of related enzymes, the tymo-like proteinases, within the proposed papain-like proteinase supergroup. The resulting alignment of 10 tymo-like proteinase sequences has revealed a third highly conserved residue--Gly (Gly821 in TYMV RP) followed by a hydrophobic residue. We speculate that all the tymo-like proteinase domains of the viral replicative proteins may share common biochemical and biological features.

Computer-assisted assignment of functional domains in the nonstructural polyprotein of hepatitis E virus: delineation of an additional group of positive-strand RNA plant and animal viruses.

Computer-assisted comparison of the nonstructural polyprotein of hepatitis E virus (HEV) with proteins of other positive-strand RNA viruses allowed the identification of the following putative functional domains: (i) RNA-dependent RNA polymerase, (ii) RNA helicase, (iii) methyltransferase, (iv) a domain of unknown function ("X" domain) flanking the papain-like protease domains in the polyproteins of animal positive-strand RNA viruses, and (v) papain-like cysteine protease domain distantly related to the putative papain-like protease of rubella virus (RubV). Comparative analysis of the polymerase and helicase sequences of positive-strand RNA viruses belonging to the so-called "alpha-like" supergroup revealed grouping between HEV, RubV, and beet necrotic yellow vein virus (BNYVV), a plant furovirus. Two additional domains have been identified: one showed significant conservation between HEV, RubV, and BNYVV, and the other showed conservation specifically between HEV and RubV. The large nonstructural proteins of HEV, RubV, and BNYVV retained similar domain organization, with the exceptions of relocation of the putative protease domain in HEV as compared to RubV and the absence of the protease and X domains in BNYVV. These observations show that HEV, RubV, and BNYVV encompass partially conserved arrays of distinctive putative functional domains, suggesting that these viruses constitute a distinct monophyletic group within the alpha-like supergroup of positive-strand RNA viruses.

Conservation of the putative methyltransferase domain: a hallmark of the 'Sindbis-like' supergroup of positive-strand RNA viruses.

Computer-assisted comparisons of the large proteins involved in the replication of viral RNA have revealed a novel domain located near the N termini of these proteins and conserved throughout the so-called 'Sindbis-like' supergroup of positive-strand RNA viruses. This domain encompasses four distinct conserved motifs, with motifs I, II and IV containing an invariant His residue, the AspXXArg signature and an invariant Tyr residue, respectively. Each of the two large groups of viruses within this supergroup, the 'altovirus' group (alphaviruses, tobamoviruses, tobraviruses, hordeiviruses, tricornaviruses, furoviruses, hepatitis E virus and probably rubiviruses), and the 'typovirus' group (tymoviruses, potexviruses, carlaviruses and apple chlorotic leaf spot virus), can be characterized by additional conserved sequence motifs. Based on the available results of biochemical studies and site-directed mutagenesis of the alphavirus proteins, it is hypothesized that this domain may be involved in methylation of the cap during viral RNA maturation. Unlike the other conserved domains, the RNA-dependent RNA polymerase and the RNA helicase, the motifs typical of the putative methyltransferase domain are universal within the Sindbis-like supergroup but are not found in the proteins of any other viruses, constituting a distinctive hallmark of this supergroup.

Unexpected close relationship between the large nonvirion proteins of filamentous potexviruses and spherical tymoviruses.

The amino acid sequences of the large proteins of potexviruses and tymoviruses were aligned. It was shown that three domains of these proteins display significant similarity between the two virus groups. In contrast to central (putative NTPase-helicase) and C-terminal (putative polymerase) domains, the conservative N-terminal domain of the potexvirus/tymovirus large protein displayed no obvious similarity to the respective regions of the large proteins of other Sindbis-like viruses.

Anomalous electrophoretic behavior of the major potato virus X RNA translation product.

The major potato virus X (PVS) RNA translation product migrates in Laemmli's electrophoresis system as a 210 kDa polypeptide ('p210'). If a Tris-phosphate-SDS buffer system is used instead of a Tris-glycine-SDS one, the mobility of p210 is higher than that of the largest TMV RNA translation product, the 183 kDa protein. It is suggested that anomalous electrophoretic behavior of the largest PVX polypeptide during SDS-electrophoresis is due to its primary structure, namely to the presence of hydrophilic domains.

Conserved and variable elements in RNA genomes of potexviruses.

The nucleotide sequences of genomic RNAs and predicted amino acid sequences of two strains of potato virus X and white clover mosaic potexvirus were compared to each other, and the proteins of different plus-RNA-containing plant viruses. The predicted non-virion proteins of potexviruses have direct sequence homology and common structural peculiarities with those of several 'Sindbis-like' plant viruses. The most conserved amino acid sequences were found to be located in the polypeptide encoded by the long 5'-proximal open reading frame (ORF1). The putative polypeptide encoded by the ORF2 starting beyond the ORF1 stop codon is clearly related to the presumptive NTP-binding domain of the ORF1-coded polypeptide. These results suggest possible functions for all of the potexvirus proteins and also indicate that potexviruses have a genome organization which is considerably different from that of other plant viruses.

An RNA-dependent nucleoside triphosphate hydrolase from Krebs-II ascites tumor cells. Detection and preliminary characterization.

A novel enzymatic activity, RNA-dependent, NTPase, was isolated from Krebs-II ascites tumor cells. This activity is associated with ribosomes and can be detached from them by washing in KCl solutions of a higher than 0.3 M concentration. The enzyme hydrolyzes all the four nucleoside triphosphates to the corresponding nucleoside diphosphates and orthophosphate. The rate of NTP hydrolysis increases about 10-fold in the presence of natural RNAs and synthetic polyribonucleotides [except poly(G)]. Natural DNAs, both double and single-stranded, are poor cofactors, although pol(dA) and poly(dT) stimulate, to a certain extent, the rate of ATP hydrolysis. Possible involvement of RNA-dependent NTPase in protein biosynthesis is discussed.