Sequence dependence of substrate recognition and cleavage by yeast RNase III

Yeast Rnt1p is a member of the double-stranded RNA (dsRNA) specific RNase III family of endoribonucleases involved in RNA processing and RNA interference (RNAi). Unlike other RNase III enzymes, which recognize a variety of RNA duplexes, Rnt1p cleaves specifically RNA stems capped with the conserved AGNN tetraloop. This unusual substrate specificity challenges the established dogma for substrate selection by RNase III and questions the dsRNA contribution to recognition by Rnt1p. Here we show that the dsRNA sequence adjacent to the tetraloop regulates Rnt1p cleavage by interfering with RNA binding. In context, sequences surrounding the cleavage site directly influence the cleavage efficiency. Introduction of sequences that stabilize the RNA helix enhanced binding while reducing the turnover rate indicating that, unlike the tetraloop, Rnt1p binding to the dsRNA helix may become rate-limiting. These results suggest that Rnt1p activity is strictly regulated by a combination of primary and tertiary structural elements allowing a substrate-specific binding and cleavage efficiency.     

Design,RNA cleavage and antiviral activity of new artificial ribonucleases derived from mono-, di- and tripeptides connected by linkers of different hydrophobicity

A novel series of metal-free artificial ribonucleases (aRNases) was designed, synthesized and assessed in terms of ribonuclease activity and ability to inactivate influenza virus WSN/A33/H1N1 in vitro. The compounds were built of two short peptide fragments, which include Lys, Ser, Arg, Glu and imidazole residues in various combinations, connected by linkers of different hydrophobicity (1,12-diaminododecane or 4,9-dioxa-1,12-diaminododecane). These compounds efficiently cleaved different RNA substrates under physiological conditions at rates three to five times higher than that of artificial ribonucleases described earlier and displayed RNase A-like cleavage specificity. aRNases with the hydrophobic 1,12-diaminododecane linker displayed ribonuclease activity 3–40 times higher than aRNases with the 4,9-dioxa-1,12-diaminododecane linker. The assumed mechanism of RNA cleavage was typical for natural ribonucleases, that is, general acid-base catalysis via the formation of acid/base pairs by functional groups of amino acids present in the aRNases; the pH profile of cleavage confirmed this mechanism. The most active aRNases under study exhibited high antiviral activity and entirely inactivated influenza virus A/WSN/33/(H1N1) after a short incubation period of viral suspension under physiological conditions.     

Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily

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Why ribonucleases induce tumor cell death

The characteristics and the possible mechanisms of action of cytotoxic ribonucleases (RNases), promising antitumor drugs, are described. Original experimental data and the results of analysis of recent publications have made it possible to identify the cellular components providing for the selective effects of exogenous RNases on tumor cells, on the one hand, and to estimate the contributions of individual molecular determinants to the enzyme cytotoxicity, on the other hand. The predominant effect of the electric charge of the RNase molecule on the induction of cell death has been demonstrated. The cytotoxic effects of RNases are determined by the catalytic cleavage of accessible RNA, the action of the products of its hydrolysis, and the noncatalytic electrostatic interaction of the exogenous enzyme with cell components. Potential RNase targets in a tumor cell and the role of modulation of calcium-dependent potassium channels and the ras oncogene in RNase-induced cell damage are considered. The effect of cytotoxic RNases on gene expression by affecting RNA interference is discussed.Translated from Molekulyarnaya Biologiya, Vol. 39, No. 1, 2005, pp. 3–13.Original Russian Text Copyright © 2005 by Ilinskaya, Makarov.     

Influence of key residues on the heterologous extracellular production of fungal ribonuclease U2 in the yeast Pichia pastoris

Ribonuclease U2, secreted by the smut fungus Ustilago sphaerogena, is a cyclizing ribonuclease that displays a rather unusual specificity within the group of microbial extracellular RNases, best represented by RNase T1. Superposition of the three-dimensional structures of RNases T1 and U2 suggests that the RNase U2 His 101 would be the residue equivalent to the RNase T1 catalytically essential His 92. RNase U2 contains three disulfide bridges but only two of them are conserved among the family of fungal extracellular RNases. The non-conserved disulfide bond is established between Cys residues 1 and 54. Mispairing of the disulfide network due to the presence of two consecutive Cys residues (54 and 55) has been invoked to explain the presence of wrongly folded RNase U2 species when produced in Pichia pastoris. In order to study both hypotheses, the RNase U2 H101Q and C1/54S variants have been produced, purified, and characterized. The results obtained support the major conclusion that His 101 is required for proper protein folding when secreted by the yeast P. pastoris. On the other hand, substitution of the first Cys residue for Ser results in a mutant version which is more efficiently processed in terms of a more complete removal of the yeast α-factor signal peptide. In addition, it has been shown that elimination of the Cys 1–Cys 54 disulfide bridge does not interfere with RNase U2 proper folding, generating a natively folded but much less stable protein.     

Influence of Auxin-Like Herbicides on Tobacco Mosaic Virus Multiplication

Tobacco (Nicotiana tabacum L., cv. Samsun) leaf discs inoculated with tobacco mosaic virus (TMV) were treated with auxin-like herbicides 2,4-dichlorophenoxyacetic acid (2,4-D), 2-methyl-4-chlorophenoxyacetic acid (MCPA), 3-amino-1,2,4-triazol (Amitrol) and 6-chloro-2-ethylamino-4-isopropylamino-1,3,5-triazine (Atrazin). All herbicides in the concentration of 10^–7 M enhanced the virus content (MCPA to 227.4 %, Amitrol to 218.1 % and Atrazin to 257.3 % of values found in TMV-infected, herbicide untreated discs). The 2,4-D alone did not affect the activity of the glucose-6-phosphate dehydrogenase and ribonucleases, but the 2,4-D treatment together with TMV infection raised their activities twice as high as in the untreated control discs. Polyacrylamide gel electrophoresis of acidic extracellular proteins washed from leaf discs treated with 2,4-D did not prove the induction of PR-proteins.     

The secreted ribonuclease T2 protein FoRnt2 contributes to Fusarium oxysporum virulence

Secreted RNase proteins have been reported from only a few pathogens, and relatively little is known about their biological functions. Fusarium oxysporum is a soilborne fungal pathogen that causes Fusarium wilt, one of the most important diseases on tomato. During the infection of F. oxysporum, some proteins are secreted that modulate host plant immunity and promote pathogen invasion. In this study, we identify an RNase, FoRnt2, from the F. oxysporum secretome that belongs to the ribonuclease T2 family. FoRnt2 possesses an N-terminal signal peptide and can be secreted from F. oxysporum. FoRnt2 exhibited ribonuclease activity and was able to degrade the host plant total RNA in vitro dependent on the active site residues H80 and H142. Deletion of the FoRnt2 gene reduced fungal virulence but had no obvious effect on mycelial growth and conidial production. The expression of FoRnt2 in tomato significantly enhanced plant susceptibility to pathogens. These data indicate that FoRnt2 is an important contributor to the virulence of F. oxysporum, possibly through the degradation of plant RNA.