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. 2003 Jun;23(12):4094-106.
doi: 10.1128/MCB.23.12.4094-4106.2003.

Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation

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Yeast Lsm1p-7p/Pat1p deadenylation-dependent mRNA-decapping factors are required for brome mosaic virus genomic RNA translation

Amine O Noueiry et al. Mol Cell Biol. 2003 Jun.

Abstract

Previously, we used the ability of the higher eukaryotic positive-strand RNA virus brome mosaic virus (BMV) to replicate in yeast to show that the yeast LSM1 gene is required for recruiting BMV RNA from translation to replication. Here we extend this observation to show that Lsm1p and other components of the Lsm1p-Lsm7p/Pat1p deadenylation-dependent mRNA decapping complex were also required for translating BMV RNAs. Inhibition of BMV RNA translation was selective, with no effect on general cellular translation. We show that viral genomic RNAs suitable for RNA replication were already distinguished from nonreplication templates at translation, well before RNA recruitment to replication. Among mRNA turnover pathways, only factors specific for deadenylated mRNA decapping were required for BMV RNA translation. Dependence on these factors was not only a consequence of the nonpolyadenylated nature of BMV RNAs but also involved the combined effects of the viral 5' and 3' noncoding regions and 2a polymerase open reading frame. High-resolution sucrose density gradient analysis showed that, while mutating factors in the Lsm1p-7p/Pat1p complex completely inhibited viral RNA translation, the levels of viral RNA associated with ribosomes were only slightly reduced in mutant yeast. This polysome association was further verified by using a conditional allele of essential translation initiation factor PRT1, which markedly decreased polysome association of viral genomic RNA in the presence or absence of an LSM7 mutation. Together, these results show that a defective Lsm1p-7p/Pat1p complex inhibits BMV RNA translation primarily by stalling or slowing the elongation of ribosomes along the viral open reading frame. Thus, factors in the Lsm1p-7p/Pat1p complex function not only in mRNA decapping but also in translation, and both translation and recruitment of BMV RNAs to viral RNA replication are regulated by a cell pathway that transfers mRNAs from translation to degradation.

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Figures

FIG. 1.
FIG. 1.
(A) Schematic diagram of the BMV genome (RNA1 to RNA3) showing ORFs (open boxes), NCRs (single lines), tRNA-like 3′ ends (cloverleaf), the subgenomic mRNA start site (bent arrow), and the subgenomic mRNA (RNA4). (B) Schematic diagram of BMV RNA translation and 1a-dependent recruitment from translation to replication on the ER.
FIG. 2.
FIG. 2.
Inhibition of RNA2 translation in lsm1Δ, lsm6Δ, lsm7Δ, and pat1Δ mutant yeast. (A and B) Northern and Western blot analysis of RNA2 and 2a protein in wt and lsm1Δ yeast (A) and in wt and lsm6Δ, lsm7Δ, and pat1Δ yeast (B). Northern blots were hybridized with positive-strand-specific RNA probes from the 2a gene. The percent wt (% WT) 2a protein values are averages of three or more experiments.
FIG. 3.
FIG. 3.
(A) Venn diagram representing relationships between yeast genes required for the deadenylation-dependent and NMD mRNA decapping and turnover pathways. The solid and dashed ellipses surround genes for deadenylation-dependent and NMD mRNA turnover pathways, respectively. Genes in the intersection are involved in both pathways. Genes not essential for survival in the yeast strain BY4742 are in boldface. (B) Northern and Western blot analysis of RNA2 and 2a protein accumulation in wt and upf1Δ, upf2Δ, and upf3Δ yeast. (C) Same as in panel B for wt and vps16Δ, edc1Δ, and edc2Δ yeast. Northern blots were hybridized with positive-strand specific RNA probes from the 2a gene. The percent wt (% WT) 2a protein values are averages of three or more experiments.
FIG. 4.
FIG. 4.
Inhibition of genomic RNA1 and RNA3 but not subgenomic RNA4 translation in LSM1/PAT1 mutant yeast. (A to C) Northern and Western blot analysis of the accumulation of RNA1 and 1a protein (A), RNA3 and 3a protein (B), and RNA4 and coat protein (C) in wt and lsm1Δ, lsm6Δ, lsm7Δ, and pat1Δ yeast. Northern blots were hybridized with positive-strand specific RNA probes for the 3′ tRNA-like ends conserved on all BMV RNAs. The percent wt (% WT) 1a, 3a, or coat protein values are averages of three or more experiments.
FIG. 5.
FIG. 5.
General cellular translation is unaffected in lsm1Δ, lsm6Δ, lsm7Δ, and pat1Δ mutant yeast. (A) Polyacrylamide gel autoradiograph (upper panel) and acid-precipitable counts (lower panel) from 35S-labeled protein extracts from wt and lsm1Δ, lsm6Δ, lsm7Δ, and pat1Δ yeast. The percent wt (% WT) acid-precipitable counts are averages of three or more experiments. (B) UV absorbance profile at 254 nm of cellular extracts from wt and lsm1Δ, lsm6Δ, lsm7Δ, and pat1Δ yeast fractionated on 10 to 50% (wt/vol) sucrose gradients. Each experiment was repeated three or more times, and representative data are shown.
FIG. 6.
FIG. 6.
Mapping of RNA2 determinants contributing to dependence of translation on LSM7. (A) Schematic diagrams of 2a mRNAs showing 2a ORF (white box), wt RNA2 5′ and 3′ NCRs (solid bars), and GAL1 mRNA 5′ and ADH1 3′ NCRs (open bars). Northern and Western blot analyses of 2a mRNA and protein accumulation in wt and lsm7Δ yeast containing these mRNAs are shown in the center. The histogram compares relative 2a protein accumulation for all combinations. Relative 2a accumulation was defined as the ratio between 2a protein and mRNA levels and was normalized to relative 2a accumulation for wt RNA2 (BMV/BMV/BMV) in wt yeast (100%). (B) Same as in panel A but for mRNAs with the 2a ORF replaced by the GFP ORF (gray box). The percent wt 2a protein values are averages of three or more experiments.
FIG. 7.
FIG. 7.
Sucrose density gradient sedimentation analysis of the ribosome and polysome association of RNA2 derivatives in wt yeast. (A) The top trace shows the UV absorbance profile at 254 nm of a cytoplasmic extract of wt yeast after sedimentation on a 10 to 50% (wt/vol) sucrose gradient. Aligned below this are Northern blots, probed for the 2a ORF, of fractions from identical gradients, centrifuged in parallel, of extracts from yeast expressing the indicated RNA2 derivatives from Fig. 6A. The bottom curves plot the amount of RNA2-derived mRNA in each fraction, expressed as a percentage of the total amount of RNA2-derived mRNA recovered over the gradient. (B) Same as in panel A but for mRNAs with the 2a ORF replaced by the GFP ORF. Each experiment was repeated three or more times, and representative data are shown. The vertical line through the UV absorbance profiles, Northern blots, and curves demarcates the point between ribosome-associated and non-ribosome-associated RNA.
FIG. 8.
FIG. 8.
Distribution of RNA2 in polysome and nonpolysome fractions in wt and lsm7Δ yeast. (A) The top trace shows the UV absorbance profile at 254 nm of a cytoplasmic extract from wt yeast expressing wt RNA2, after sedimentation on a 10 to 50% sucrose gradient. Aligned below this are Northern blots of RNA2 in fractions from identical gradients, centrifuged in parallel, of extracts of wt and lsm7Δ yeast expressing RNA2. The bottom curves plot the amount of RNA2 in each fraction, expressed as a percentage of the total amount of RNA2 recovered over the gradient. The inset in the lower panel plots samples 10 to 29 on an expanded scale of 0 to 4% total RNA2. The vertical line through the UV absorbance profiles, Northern blots, and curves demarcates the point between ribosome-associated and non-ribosome-associated RNA. (B) Coincidence of RNA2 with ribosome peaks in polysome fractions. UV absorbance profile at 254 nm of cellular extracts from lsm7Δ yeast expressing RNA2 (solid line) and quantitation of Northern blot analysis of small fractions in the middle of the gradient (dotted line). The amount of RNA2 in each fraction is expressed as a percentage of the total amount of RNA2 recovered in these fractions. Each experiment was repeated three or more times, and representative data are shown. (C) The traces in the top panel show the UV absorbance profile at 254 nm of a cytoplasmic extract from lsm7Δ yeast expressing wt RNA2, after sedimentation on a 10 to 50% sucrose gradient without EDTA (solid line) and with EDTA (dashed line). Aligned below this are Northern blots of RNA2 in fractions from these gradients, centrifuged in parallel. The bottom curves plot the amount of RNA2 in each fraction, expressed as a percentage of the total amount of RNA2 recovered over the gradient. The inset in the lower panel plots samples 9 to 30 on an expanded scale of 0 to 4% total RNA2. The vertical lines through the UV absorbance profiles, Northern blots, and curves demarcate the point between ribosome-associated and non-ribosome-associated RNA.
FIG. 9.
FIG. 9.
Distribution of RNA2 in polysome and nonpolysome fractions in wt (A), lsm7Δ (B), prt1-1 (C), and lsm7Δ/prt1-1 (D) yeast at 26 and 37°C. The traces in the top panels show the UV absorbance profiles at 254 nm of cytoplasmic extracts from the relevant yeast strains expressing wt RNA2 grown at 26°C (solid lines) and grown at 26°C, followed by incubation at 37°C for 30 min (dotted lines), after sedimentation on a 10 to 50% sucrose gradient. Aligned below this are Northern blots of RNA2 in fractions from these gradients, centrifuged in parallel. The bottom curves plot the amount of RNA2 in each fraction, expressed as a percentage of the total amount of RNA2 recovered over the gradient. The insets in lower panels of panels C and D plot samples 8 to 30 on an expanded scale of 0 to 6% total RNA2.

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