Recent experiments have defined cytoplasmic foci, referred to as processing bodies (P-bodies), wherein mRNA decay factors are concentrated and where mRNA decay can occur. However, the physical nature of P-bodies, their relationship to translation, and possible roles of P-bodies in cellular responses remain unclear. We describe four properties of yeast P-bodies that indicate that P-bodies are dynamic structures that contain nontranslating mRNAs and function during cellular responses to stress. First, in vivo and in vitro analysis indicates that P-bodies are dependent on RNA for their formation. Second, the number and size of P-bodies vary in response to glucose deprivation, osmotic stress, exposure to ultraviolet light, and the stage of cell growth. Third, P-bodies vary with the status of the cellular translation machinery. Inhibition of translation initiation by mutations, or cellular stress, results in increased P-bodies. In contrast, inhibition of translation elongation, thereby trapping the mRNA in polysomes, leads to dissociation of P-bodies. Fourth, multiple translation factors and ribosomal proteins are lacking from P-bodies. These results suggest additional biological roles of P-bodies in addition to being sites of mRNA degradation.

Eukaryotic cells contain nontranslating messenger RNA concentrated in P-bodies, which are sites where the mRNA can be decapped and degraded. We present evidence that mRNA molecules within yeast P-bodies can also return to translation. First, inhibiting delivery of new mRNAs to P-bodies leads to their disassembly independent of mRNA decay. Second, P-bodies decline in a translation initiation-dependent manner during stress recovery. Third, reporter mRNAs concentrate in P-bodies when translation initiation is blocked and resume translation and exit P-bodies when translation is restored. Fourth, stationary phase yeast have large P-bodies containing mRNAs that reenter translation when growth resumes. The reciprocal movement of mRNAs between polysomes and Pbodies is likely to be important in the control of mRNA translation and degradation. Moreover, the presence of related proteins in P-bodies and maternal mRNA storage granules suggests this mechanism is widely adapted for mRNA storage.A key aspect of the regulation of eukaryotic gene expression is the control of mRNA translation and degradation, which often occurs by decapping, followed by 5′ to 3′ decay (1). Translation and mRNA degradation via decapping are tightly linked. To decap, an mRNA exits translation and assembles into a translationally repressed messenger ribonucleoprotein (mRNP) lacking translation initiation factors and containing the decapping enzyme and several accessory proteins (1,2). These translationally repressed mRNPs accumulate within P-bodies (also referred to as GW or Dcp bodies) (3-8), where decapping can occur (9,10). The formation of a P-body mRNP is also important for control of translational repression (2,11,12). An unresolved issue is whether P-bodies can store mRNAs and later release them to reenter translation.To determine whether mRNAs in P-bodies were committed to decapping, we examined Pbodies in dcp1Δ cells where decapping is blocked (1) after 10 min of cycloheximide treatment, which prevents mRNAs from exiting translation and entering P-bodies (7,9,10,13). We directly observed P-body proteins by using green fluorescent protein (GFP)-tagged versions of the components Dcp2p and Dhh1p, whose presence in P-bodies is dependent on RNA, thus also providing an indirect manner of observing P-body mRNAs (7). We observed that P-bodies in dcp1Δ (Fig. 1A) and xrn1Δ cells (fig. S1) declined after cycloheximide treatment, suggesting that mRNPs can exit P-bodies in the absence of decapping and 5′ to 3′ degradation.

Recent experiments have shown that mRNAs can move between polysomes and P-bodies, which are aggregates of nontranslating mRNAs associated with translational repressors and the mRNA decapping machinery. The transitions between polysomes and P-bodies and how the poly(A) tail and the associated poly(A) binding protein 1 (Pab1p) may affect this process are unknown. Herein, we provide evidence that poly(A)؉ mRNAs can enter P-bodies in yeast. First, we show that both poly(A)؊ and poly(A) ؉ mRNA become translationally repressed during glucose deprivation, where mRNAs accumulate in P-bodies. In addition, both poly(A) ؉ transcripts and/or Pab1p can be detected in P-bodies during glucose deprivation and in stationary phase. Cells lacking Pab1p have enlarged P-bodies, suggesting that Pab1p plays a direct or indirect role in shifting the equilibrium of mRNAs away from P-bodies and into translation, perhaps by aiding in the assembly of a type of mRNP within P-bodies that is poised to reenter translation. Consistent with this latter possibility, we observed the translation initiation factors (eIF)4E and eIF4G in P-bodies at a low level during glucose deprivation and at high levels in stationary phase. Moreover, Pab1p exited P-bodies much faster than Dcp2p when stationary phase cells were given fresh nutrients. Together, these results suggest that polyadenylated mRNAs can enter P-bodies, and an mRNP complex including poly(A) ؉ mRNA, Pab1p, eIF4E, and eIF4G2 may represent a transition state during the process of mRNAs exchanging between P-bodies and translation. INTRODUCTIONThe regulation of mRNA translation and degradation is an important aspect of the control of eukaryotic gene expression. In yeast, the major pathway of mRNA degradation is initiated by shortening of the 3Ј poly(A) tail (deadenylation), followed by decapping by the Dcp1/Dcp2 decapping complex, thereby exposing the transcript to a 5Ј-to-3Ј degradation by the exonuclease Xrn1p (for review, see Coller and Parker, 2004). Decapping is a key step of this process, because it precedes and permits the degradation of the body of the mRNA and represents the site of multiple control inputs.The processes of mRNA decapping and translation are mechanistically intertwined and seem to compete with each other, at least in yeast (for review, see Coller and Parker, 2004). For example, decreasing translation initiation by a variety of means increases the rate of mRNA decapping (LaGrandeur and Parker, 1999;Muhlrad and Parker, 1999;Schwartz and Parker, 1999). Conversely, an inhibition of translation elongation leads to a significant decrease in the rate of decapping (Beelman and Parker, 1994). Moreover, coimmunoprecipitation experiments suggested that before decapping, an mRNA exits translation and then assembles into a translationally repressed messenger ribonucleoprotein (mRNP) complex (Tharun and Parker, 2001).Additional evidence for a discrete population of nontranslating mRNPs has been that nontranslating mRNAs, and the decapping machinery, accumulate in discrete cytoplasmic fo...