Host Ribosomes Research Articles

The N-Glycosidase Activity of the Ribosome-inactivating Protein ME1 Targets Single-stranded Regions of Nucleic Acids Independent of Sequence or Structural Motifs

ME(1), a type I ribosome-inactivating protein (RIP), belongs to a family of enzymes long believed to possess rRNA N-glycosidase activity directed solely at the universally conserved residue A4324 in the sarcin/ricin loop of large eukaryotic and prokaryotic rRNAs. We have investigated the effect of modifying the structure of nonribosomal RNA substrates on their interaction with ME(1) and other RIPs. ME(1) was shown to depurinate a variety of partially denatured nucleic acids, randomly removing adenine residues from single-stranded regions and, to a lesser extent, guanine residues from wobble base-pairs in hairpin stems. A defined sequence motif was not required for recognition of non-paired adenosines and cleavage of the N-glycosidic bond. Substrate recognition and ME(1) activity appeared to depend on the physical availability of nucleotides, and denaturation of nucleic acid substrates increased their interaction with ME(1). Pretreatment of mRNA at 75 degrees C rather than 60 degrees C, for example, lowered the apparent K(D) from 87.1 to 73.9 nm, making it more vulnerable to depurination by RIPs. Exposure to ME(1) in vitro completely abolished the infectivity of partially denatured RNA transcripts of the potato spindle tuber viroid, suggesting that RIPs may target invading nucleic acids before they reach host ribosomes in vivo. Our data suggest that the extensive folding of many potential substrates interferes with their ability to interact with RIPs, thereby blocking their inactivation by ME(1) (or other RIPs).

TRNA-like structure regulates translation of Brome mosaic virus RNA.

For various groups of plant viruses, the genomic RNAs end with a tRNA-like structure (TLS) instead of the 3' poly(A) tail of common mRNAs. The actual function of these TLSs has long been enigmatic. Recently, however, it became clear that for turnip yellow mosaic virus, a tymovirus, the valylated TLS(TYMV) of the single genomic RNA functions as a bait for host ribosomes and directs them to the internal initiation site of translation (with N-terminal valine) of the second open reading frame for the polyprotein. This discovery prompted us to investigate whether the much larger TLSs of a different genus of viruses have a comparable function in translation. Brome mosaic virus (BMV), a bromovirus, has a tripartite RNA genome with a subgenomic RNA4 for coat protein expression. All four RNAs carry a highly conserved and bulky 3' TLS(BMV) (about 200 nucleotides) with determinants for tyrosylation. We discovered TLS(BMV)-catalyzed self-tyrosylation of the tyrosyl-tRNA synthetase but could not clearly detect tyrosine incorporation into any virus-encoded protein. We established that BMV proteins do not need TLS(BMV) tyrosylation for their initiation. However, disruption of the TLSs strongly reduced the translation of genomic RNA1, RNA2, and less strongly, RNA3, whereas coat protein expression from RNA4 remained unaffected. This aberrant translation could be partially restored by providing the TLS(BMV) in trans. Intriguingly, a subdomain of the TLS(BMV) could even almost fully restore translation to the original pattern. We discuss here a model with a central and dominant role for the TLS(BMV) during the BMV infection cycle.

Third Position Codon Composition Suggests Two Classes of Genes Within the Cauliflower Mosaic Virus Genome

The translation of viral mRNAs by host ribosomes is essential for infection. Hence, codon usage of virus genes may influence efficiency of infection. In addition, composition of nucleotides in the third position within codons of genes can reflect evolutionary relationships. In this study, third position codon composition was examined for the seven genes of eight Cauliflower mosaic virus isolates. Genes IV–VII had similar codon composition values and were termed Class 1 genes. Genes I–III possessed corresponding codon composition values and were termed Class 2 genes. The codon composition values of Class 1 and genes differed significantly. Neither Class 1 nor Class 2 genes had codon composition values identical to that of the host plant, Arabidopsis thaliana. However, Class 1 genes possessed codon composition values closer to those of the host than Class 2 genes. Examination of the genomes of three Rous sarcoma virus isolates indicated that codon composition values were similar for the gag, pol, and env genes but these genes differed significantly from the src genes. Since codon composition values for Rous sarcoma virus distinguished a “foreign” gene from the rest of the viral genome, it is possible that the Cauliflower mosaic virus genome is composed of genes from two different sources. Others have suggested that Cauliflower mosaic virus evolved in this manner and our data provide support for this hypothesis.

A potential RNA drug target in the hepatitis C virus internal ribosomal entry site.

Subdomain IlId from the hepatitis C virus (HCV) internal ribosome entry site (IRES) has been shown to be essential for cap-independent translation. We have conducted a structural study of a 27-nt fragment, identical in sequence to IlId, to explore the structural features of this subdomain. The proposed secondary structure of IlId is comprised of two 3 bp helical regions separated by an internal loop and closed at one end by a 6-nt terminal loop. NMR and molecular modeling were used interactively to formulate a validated model of the three-dimensional structure of IlId. We found that this fragment contains several noncanonical structural motifs and non-Watson-Crick base pairs, some of which are common to other RNAs. In particular, a motif characteristic of the rRNA alpha-sarcin/ricin loop was located in the internal loop. The terminal loop, 5'-UUGGGU, was found to fold to form a trinucleotide loop closed by a trans-wobble U.G base pair. The sixth nucleotide was bulged out to allow stacking of this U.G pair on the adjacent helical region. In vivo mutational analysis in the context of the full IRES confirmed the importance of each structural motif within IIId for IRES function. These findings may provide clues as to host cellular proteins that play a role in IRES-directed translation and, in particular, the mechanism through which host ribosomes are sequestered for viral function.

A novel mechanism for inhibition of translation by pokeweed antiviral protein: depurination of the capped RNA template.

Pokeweed antiviral protein (PAP) is known to inactivate ribosomes by removal of a specific adenine from the sarcin/ricin (S/R) loop of the large rRNA, thereby inhibiting translation. We demonstrate here that in addition to the previously identified adenine (A4324), PAP removes another adenine (A4321) and a guanine (G4323) from the eukaryotic large rRNA. Recent results indicate that the antiviral activity of PAP may not be due to depurination of host ribosomes. Using PAP mutants that do not depurinate either tobacco or reticulocyte lysate rRNA, we show that PAP inhibits translation of brome mosaic virus (BMV) and potato virus X (PVX) RNAs without depurinating ribosomes. Furthermore, translation of only capped, but not uncapped, luciferase transcripts is inhibited by PAP, providing evidence that PAP and PAP mutants are able to distinguish between capped and uncapped transcripts. Translation inhibition of BMV RNAs is overcome by treatment with PAP in the presence of increasing concentrations of the cap analog m7GpppG, but not GpppG or GTP, indicating that PAP recognizes the cap structure. Incubation of BMV RNAs or the capped luciferase transcripts with PAP results in depurination of either RNA. In contrast, uncapped luciferase transcripts are not depurinated after incubation with identical concentrations of PAP. These results demonstrate for the first time that PAP can inhibit translation by a mechanism other than ribosome depurination, by recognizing the cap structure and specifically depurinating the capped RNAs.

C-terminal deletion mutant of pokeweed antiviral protein inhibits viral infection but does not depurinate host ribosomes.

Pokeweed antiviral protein (PAP), a 29-kDa protein isolated from Phytolacca americana, inhibits translation by catalytically removing a specific adenine residue from the large rRNA of the 60S subunit of eukaryotic ribosomes. In addition to its ribosome-inactivating ability, PAP has potent antiviral activity against many plant and animal viruses, including HIV. We recently described the isolation and characterization of nontoxic PAP mutants, NT123-2, which has a point mutation (E176V) in the active site that abolishes enzymatic activity, and NT124-3, which has a nonsense mutation that results in deletion of the C-terminal 25 aa (W237Stop). In vitro translation of rabbit reticulocyte lysate ribosomes was inhibited by the C-terminal deletion mutant, but not by the active site mutant. We expressed both mutants in transgenic tobacco and showed that, unlike PAP or variant PAP, neither mutant is toxic to transgenic plants. In vivo depurination of rRNA was detected in transgenic tobacco expressing variant PAP, but not in transgenic plants expressing either the active site mutant or the C-terminal deletion mutant PAP. When extracts from transgenic plants containing the mutant PAPs were exogenously applied to tobacco leaves in the presence of potato virus X (PVX), the C-terminal deletion mutant had antiviral activity, while the active site mutant had no antiviral activity. Furthermore, transgenic plants expressing low levels of the C-terminal deletion mutant showed resistance to PVX infection, while transgenic plants expressing very high levels of the active site mutant PAP were not resistant to PVX. Our results demonstrate that an intact active site of PAP is necessary for antiviral activity, toxicity, and in vivo depurination of tobacco ribosomes. However, an intact active site is not sufficient for all these activities. An intact C terminus is also required for toxicity and depurination of tobacco ribosomes in vivo, but not for antiviral activity, suggesting that antiviral activity of PAP can be dissociated from its toxicity.

A possible mechanism for the antiviral activity of pokeweed antiviral protein

The mechanism by which pokeweed antiviral protein (PAP) inhibits the infection of tobacco by TMV was investigated. The N-glycosidase activity of PAP was measured using a combination of aniline treatment to cleave the rRNA at the depurinated site, gel electrophoresis and Northern blot hybridization using a probe specific for the 3′ end of tobacco 25S rRNA. Using this assay it was found that the host ribosomes, which are used by viruses to uncoat and to synthesize replicases at an early stage of infection, were depurinated and probably inactivated by PAP as early as 5 min after inoculation. It was also found that the extent of the inhibition of virus infection and the depurination of host ribosomes were positively correlated with the concentration of PAP. These results suggest that the depurination and inactivation of host ribosomes is the cause of the inhibition of virus infection by PAP.

Specificities of RNA N-glycosidase activity of Mirabilis antiviral protein variants.

Mirabilis antiviral protein (MAP), a ribosome-inactivating protein, inactivates both eukaryotic and prokaryotic ribosomes by means of site-specific RNA N-glycosidase activity. In order to identify the site of this activity, some amino acid residues of MAP, conserved in homologous ribosome-inactivating proteins, were altered to other amino acids by replacing DNA fragments of the total synthetic gene of MAP. When the in vitro proteins synthesis of rabbit reticulocyte was treated with MAP variants secreted into culture media of Escherichia coli transformants, the inhibitory effect of R26L and R48L (R26L designates MAP variant with Arg-26 changed to Leu) was found to be similar to that of native MAP. Both purified Y72F and Y118F had the same effect as native MAP, and E168D had a slightly weaker effect. In contrast, on the protein synthesis of E. coli, Y118F had one-tenth the effect of native MAP, and Y72F and E168D approximately one-hundredth the effect. These three variant proteins also exhibited reduced RNA N-glycosidase activity on substrate E. coli ribosomes. These results suggest that Tyr-72 and Glu-168 are involved in RNA N-glycosidase activity. When the R171K gene was expressed in E. coli, an N-glycosidic bond of the 23 S rRNA of the host ribosome was found to be cleaved, although no product of the gene could be detected. This suggests that MAP variants can maintain their N-glycosidase activity when the conserved Glu-168 and Arg-171 are changed to similarly charged residues.

Plasmid presence changes the relative levels of many host cell proteins and ribosome components in recombinant Escherichia coli

Relative levels of many individual proteins in Escherichia coli HB101 strains with 0, 37, 56, and 240 plasmids per chromosome were determined by computer image analysis of two-dimensional gel electrophoresis patterns. The plasmids investigated had very similar sequences except for small domains encoding the repressor of plasmid replication. At the intermediate plasmid copy number of 56, levels of several of the TCA cycle enzymes (oxoglutarate dehydrogenase complex, succinate thiokinase, and succinate dehydrogenase) as well as in aspartate transcarbamoylase increased. At a plasmid copy number of 240, higher amounts of PEP carboxylase as well as several of the heat shock proteins were observed. Furthermore, at high plasmid levels, significant decreases occurred in growth rate, pyruvate kinase I, pyruvate dehydrogenase complex, unadenylated glutamine synthetase, aspartate transcarbamoylase as well as in several of the proteins involved in translation. Decreases in ribosome content as well as in the free 30S and 50S ribosomal subunit pool fractions were also observed in separate analyses. These results indicate that recombinant DNA manipulations can cause major alterations in numerous host cell properties which could significantly influence cloned protein production or metabolic engineering endeavors.

Study of the function of Escherichia coli ribosomal RNA through site-directed mutagenesis

Various approaches have been developed to study how mutations in Escherichia coli ribosomal RNA affect the function of the ribosome. Most of them are in vivo approaches, where mutations are introduced in a specialized plasmid harboring the ribosomal RNA genes. The mutated plasmids are then expressed in an appropriate host, where they can confer resistance to antibiotics whose target is the ribosome. Conditions can be used where the host ribosomal RNA genes or the host ribosomes are selectively inactivated, and the effect of the mutations on ribosome assembly and function can be studied. Another approach, which has been developed mainly with 16S ribosomal RNA, can be used entirely in vitro. In this approach, a plasmid has been constructed which contains the 16S ribosomal RNA gene under control of a T7 promoter. Mutations can be introduced in the 16S ribosomal RNA sequence and the mutated 16S ribosomal RNAs are produced by in vitro transcription. It is then possible to investigate how the mutations affect the assembly of the 16S ribosomal RNA into 30S subunits and the activity of the reconstituted 30S subunits in cell-free protein synthesis assays. Although these approaches are recent, they have already provided a large body of interesting information, relating specific RNA sequences to interactions with ribosomal proteins, to ribosome function, and to its response to antibiotics.

Susceptibility of Giardia lamblia to aminoglycoside protein synthesis inhibitors: correlation with rRNA structure.

The very limited development of antiparasitic agents targeting protein synthesis stems in part from the belief that parasite and host ribosomes are sufficiently similar to preclude selective toxicity. However, recent studies have revealed that Giardia lamblia rRNA has an unusual size and sequence; consequently, this organism and its homogeneous rRNA provide a useful model for the development of protein synthesis inhibitors with antiparasitic activity. In this study, I determined the sequence and secondary structure of the 3' end of the small-subunit RNA, the target for aminoglycoside inhibitory activity. The primary structure of these 140 nucleotides includes two blocks of sequence highly conserved among other organisms; the remaining sequence, although not conserved, can be folded into a secondary structure common to all rRNAs. The presence of U-1495 within one of the conserved blocks predicts hygromycin susceptibility. Also, a specific base pair (C-1409.G-1491) implicated in paromomycin susceptibility is present; whereas all procaryotes have this base pair, it is absent in many eucaryotes (including mammals). Conversely, kanamycin and apramycin resistance can be predicted from substitution of A-1408 with G. A growth inhibition assay was used to test the susceptibility of G. lamblia to a variety of aminoglycosides. After 48 h, 8 of 11 aminoglycosides tested failed to inhibit growth at a concentration of 200 micrograms/ml. Paromomycin and hygromycin, however, inhibited growth of three strains tested by 50% at 50 to 60 micrograms/ml and by close to 90% at 120 micrograms/ml. These results correlate well with the sequence and secondary-structure analyses. Paromomycin may be clinically useful when the toxicity of standard antigiardial drugs is of concern.

Evidence for major differences in ribosomal subunit proteins from Plasmodium bergh [formula omitted] and rat liver

Purified polysomes were isolated in high yield from the erythrocytic stages of the rodent malaria parasite, Plasmodium berghei, and from rat liver. Proteins extracted from the ribosomal subunits derived from these polysomes were fractionated and their number and molecular weights were estimated by two-dimensional polyacrylamide gel electrophoresis. Plasmodial small ribosomal subunits contained 30 proteins ranging in apparent molecular size from 11.7 to 40.7 kDa, while large subunits contained 35–36 proteins ranging from 12.1 to 42.6 kDa. None of these parasite proteins was shared by the two subunits nor altered in electrophoretic mobility by radioiodination. Rat liver 40 S ribosomal subunit proteins numbered 30 and ranged from 9.2 to 37.5 kDa, while liver 60 S subunits contained 41–43 proteins with apparent molecular sizes of 10.3–45.2 kDa. Coelectrophoresis of trace amounts of radioiodinated P. berghei ribosomal subunit proteins and stainable quantities of liver proteins demonstrated that most of these 139 parasite and host ribosomal proteins possessed different two-dimensional electrophoretic mobilities under the conditions of this study. Based upon a comparative analysis of P. berghei and rodent ribosomal RNA and these data, it was concluded that parasite and host ribosomes contain distinct ribosomal RNAs and ribosomal proteins.

The ribosomes of Plasmodium berghei: isolation and ribosomal ribonucleic acid analysis

Ribosomes and high molecular weight ribosomal ribonucleic acid (rRNA) from the blood stages of Plasmodium berghei parasites were studied in preparations free from host ribosome contamination. Purified malarial ribosomes were isolated in high yield from a population of ultrastructurally intact, viable parasites by hypertonic lysis with Triton X-100 and differential centrifugation. These ribosomes were shown to be derived from active polysomes and could be dissociated into subunits by puromycin-0.5 M KCl treatment. Malarial rRNA extracted from purified 40S and 60S ribosomal subunits was characterized by electrophoretic, sedimentation and base ratio analyses. Like certain other protozoa, the P. berghei 40S ribosomal subunit possessed an exceptionally large RNA species (mol. wt 0.9 X 10(6), while RNA isolated from the parasite's 60S subunit (mol. wt 1.5 X 10(6)) was specifically 'nicked' to produce one large component (mol.wt 1.2 X 10(6)) and one small component (mol.wt 0.3 X 10(6)) in equimolar quantities. These rRNA's migrate identically on polyacrylamide gels after heating to 63 degrees C for 5 min or under denaturing conditions in the presence of formamide, indicating an absence of aggregation and non-specific degradation of the rRNA species. Base composition studies showed P. berghei rRNA to be low in guanosine and cytosine content, as is the case for protozoa generally.

The Plasmodium lophurae (avian malaria) ribosome.

Ribosomes were isolated from Plasmodium lophurae by Triton X-100 lysis and ultracentrifugation. Plasmodium lophurae ribosomal subparticles, produced by treatment of ribosomes with puromycin, were separated by sucrose gradient centrifugation. The nucleotide base composition of P. lophurae ribosomal RNA (rRNA) from intact ribosomes and subparticels was low in guanine-cytosine content (approximately 37% G + C) whereas the rRNA of the host cell (duck reticulocyte) was considerably higher (64% G + C). The rRNA of the malaria parasite was typically protozoan, with sedimentation values of 25S and 17S. In vitro, free parasites and malaria-infected red cells incorporated radioactive adenosine into both the large and the small plasmodial subparticles; label was also recovered in the 25S and 17S RNAs. These results suggest that host ribosomes do not contribute to ribosome biogenesis in this malaria, rather parasite rRNA is the transcription product of plasmodial cistrons.

Preliminary experiments to determine which host ribosomes are used by some further plant viruses.

Cycloheximide, but not chloramphenicol, greatly decreases the incorporation of radioactive amino acids into the particles of broad bean mottle virus, eggplant mosaic virus, and the type and U5 strains

Messenger selection by bacterial ribosomes.

The counterpart of Escherichia coli initiation factor 3(IF-3) was isolated from Caulobacter crescentus, purified to homogeneity, and used in comparative studies on in vitro translation of RNA from the C. crescentus RNA phage Cb5 and of coliphage MS2 RNA. The two phage RNAs are similar in physical properties and analogous in genetic content. The factor, C-IF-3, substitutes for E. coli IF-3 and promotes correct translation of MS2 RNA by E. coli ribosomes. Conversely, E. coli IF-3 substitutes for C-IF-3 in translation of Cb5 RNA by C. crescentus ribosomes. However, each phage RNA could be translated only by host ribosomes or by mixed ribosomes containing the host 30S subunit. C-IF-3 dissociates C. crescentus and E. coli 70S ribosomes into subunits. It binds phage, ribosomal, and, less efficiently, transfer RNA.

Viral RNAs associated with ribosomes in Sindbis virus-infected HeLa cells.

Virus specific RNA ribosome complexes were isolated by sucrose density gradient centrifugation of cytoplasmic extracts from HeLa cells infected at 42 C with an RNA(+) mutant (ts2) of Sindbis virus. Viral RNA-ribosome complexes were accumulated by infected cells treated with sodium fluoride and cycloheximide. The RNA-ribosome complexes were characterized by (i) their sensitivity to the action of ribonuclease or ethylenediaminetetraacetic acid, (ii) their density in cesium chloride gradients, and (iii) presence of host ribosomes and viral RNAs. The viral RNAs were isolated and characterized. The results showed that two species of single-stranded RNAs (a 28s and 18 to 15s species) were associated with the complexes. Base composition analysis of the viral RNAs indicated that both species had a higher adenine content than the 42s or 26s forms of viral RNAs. The RNAs associated with the ribosome complexes were virus specific since they annealed with denatured double-stranded RNAs from the infected cells. Little or no 42S RNA was associated with the RNA-ribosome complexes. The results suggest that the 28s and 18 to 15s forms of RNAs may represent viral messenger RNAs.

In vitro initiation of coliphage T7 mRNA

The synthesis of two classes of late T7 proteins appears to be directed by several polycistronic messenger RNAs. To understand how they are translated in appropriate order during phage infection, we have isolated late mRNA from T7-infected cells and mRNA that was synthesized in vitro with the T7 RNA polymerase and T7 DNA. Using a purified cell-free system in which ribosomal interaction with the message is restricted to the authentic phage initiation sites, we find that late T7 mRNA directs the synthesis of two initiation dipeptides, formylmethionine-alanine and formylmethionine-serine. These dipeptides account for 80% of the incorporated fMet and are synthesized in systems derived from both uninfected and infected female Escherichia coli cells. However, ribosomes isolated from T7-infected female cells apparently contain mRNA corresponding to these same T7 initiation regions since they also direct the endogenous synthesis of formylmethionine-alanine and formylmethionine-serine. This capability increases as a function of time after infection. In contrast, neither uninfected host ribosomes, ribosomes from T7 am23 (gene 1 mutant lacking T7 RNA polymerase) infected cells, ribosomes from T7-infected male host cells nor ribosomes from cells infected with Qβ RNA phage direct the synthesis of these or other formylmethionine-dipeptides. It is concluded that the ribosomes after T7 infection seem to have a high affinity for the late viral message and that the regions coding for these formylmethionine-dipeptides may represent preferred sites for their entrance on to the message.

Selective translation of T4 template RNA by ribosomes from T4-infected Escherichia coli.

The present studies indicate that T4 infection induces an alteration in host ribosomes which restricts the translation of host and other T4-unrelated template RNAs but permits normal translation of T4 RNA. A heat-labile factor has been isolated from T4-infected cell ribosomes which, when combined with normal cell ribosomes, confers upon the latter the property of selective T4 template RNA translation.