Degradation of Stable RNA in Bacteria

At first glance, the title of this minireview might appear to be an oxymoron. How can “stable” RNAs be degraded? We have become accustomed to thinking about the stable RNAs, primarily rRNA and tRNA, as being stable in an absolute sense; however, this terminology really is correct only in comparison to the rapid turnover of mRNAs. In fact, although rRNA and tRNA are quite stable during exponential growth (1Neidhardt F.C. Prog. Nucleic Acids Res. Mol. Biol. 1964; 3: 145-181Crossref PubMed Scopus (39) Google Scholar), it has been known since the earliest studies of RNA metabolism that under certain physiological conditions these RNA molecules can be extensively degraded (2Mandelstam J. Bacteriol. Rev. 1960; 24: 289-308Crossref PubMed Google Scholar). Yet, in contrast to the many studies of mRNA decay (3Steege D. RNA. 2000; 6: 1079-1090Crossref PubMed Scopus (122) Google Scholar, 4Kennell D. J. Bacteriol. 2002; 184: 4645-4657Crossref PubMed Scopus (38) Google Scholar, 5Kushner S.R. J. Bacteriol. 2002; 184: 4658-4665Crossref PubMed Scopus (198) Google Scholar), there has been relatively little attention in recent years to the study of the processes that result in degradation of stable RNAs despite the fact that these molecules account for ∼98% of all cellular RNA (6Bremer H. Dennis P.P. Neidhardt F.C. Escherichia coli and Salmonella. ASM Press, Washington, D. C1996: 1553-1569Google Scholar). Degradation of stable RNA is most usually associated with conditions of starvation. Thus, depletion of any one of a number of nutrients including phosphate (7Maruyama H. Mizuno D. Biochim. Biophys. Acta. 1970; 199: 159-165Crossref PubMed Scopus (23) Google Scholar), nitrogen (8Ben-Hamida F. Schlessinger D. Biochim. Biophys. Acta. 1966; 119: 183-191Crossref PubMed Scopus (38) Google Scholar), carbon (9Jacobson A. Gillespie D. J. Bacteriol. 1968; 95: 1030-1039Crossref PubMed Google Scholar), or even Mg2+ (10McCarthy B.J. Biochim. Biophys. Acta. 1962; 55: 880-888Crossref Scopus (56) Google Scholar) leads to a dramatic loss of RNA. It is not clear whether starvation for different nutrients leads to different rates of degradation, as data on this point have been inconsistent (e.g. Refs. 11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar and 12Kaplan R. Apirion D. J. Biol. Chem. 1975; 250: 1854-1863Abstract Full Text PDF PubMed Google Scholar). Inasmuch as ribosomes account for the bulk of cellular RNA (6Bremer H. Dennis P.P. Neidhardt F.C. Escherichia coli and Salmonella. ASM Press, Washington, D. C1996: 1553-1569Google Scholar), degradation during starvation is confined largely to rRNA. In fact, there is some evidence that tRNA may be stable under these conditions (11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar). Likewise, it appears that ribosomal proteins remain relatively stable (9Jacobson A. Gillespie D. J. Bacteriol. 1968; 95: 1030-1039Crossref PubMed Google Scholar, 12Kaplan R. Apirion D. J. Biol. Chem. 1975; 250: 1854-1863Abstract Full Text PDF PubMed Google Scholar, 13Ramagopal S. Eur. J. Biochem. 1984; 140: 353-361Crossref PubMed Scopus (13) Google Scholar) so ribosomes may be able to reassemble as soon as rRNA is synthesized. This would be important for cells to recover from starvation more rapidly because if few ribosomes remained, resynthesis of ribosomal proteins would be expected to be slow. Because ribosomes represent such a large fraction of cellular mass (6Bremer H. Dennis P.P. Neidhardt F.C. Escherichia coli and Salmonella. ASM Press, Washington, D. C1996: 1553-1569Google Scholar), they are a major storehouse for nutrients, and the ability of cells to recover from starvation may be related to their capacity to generate nutrients from degraded ribosomes (12Kaplan R. Apirion D. J. Biol. Chem. 1975; 250: 1854-1863Abstract Full Text PDF PubMed Google Scholar). Degradation of ribosomes during starvation can be rapid and quite extensive, amounting to >95% in some studies (11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar, 13Ramagopal S. Eur. J. Biochem. 1984; 140: 353-361Crossref PubMed Scopus (13) Google Scholar). Interestingly, ribosome degradation appears to be an “all or none” phenomenon in that once breakdown of a ribosome begins, it goes to completion, whereas residual ribosomes remain intact (9Jacobson A. Gillespie D. J. Bacteriol. 1968; 95: 1030-1039Crossref PubMed Google Scholar, 11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar, 12Kaplan R. Apirion D. J. Biol. Chem. 1975; 250: 1854-1863Abstract Full Text PDF PubMed Google Scholar). Some evidence suggests that 30 S subunits may disappear more rapidly than 50 S (11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar), but this is not a uniform finding (9Jacobson A. Gillespie D. J. Bacteriol. 1968; 95: 1030-1039Crossref PubMed Google Scholar). Although not conclusively established, the pathway of ribosome degradation upon starvation appears to proceed from polysomes to monosomes to ribosome subunits (12Kaplan R. Apirion D. J. Biol. Chem. 1975; 250: 1854-1863Abstract Full Text PDF PubMed Google Scholar). However, the signals controlling this progression are not known. Most studies of starvation employ a regimen in which growing cells are resuspended in medium or buffer lacking a particular nutrient. However, it has been pointed out that this is unnatural and that cells normally would lose nutrients gradually, allowing for adaptive changes that might affect subsequent events (11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar). It is not understood to what extent these laboratory regimens for starvation may affect rates or extents of RNA degradation. Nevertheless, it is clear that RNA degradation begins as soon as nutrients become limiting and before growth ceases and cell viability begins to decrease (11Davis B.D. Luger S.M. Tai P.C. J. Bacteriol. 1986; 166: 439-445Crossref PubMed Google Scholar). In Salmonella strains, rRNA degradation is taken to extremes. More than 90% of 23 S rRNA and ∼50% of 16 S rRNA are degraded when cells reach stationary phase (14Hsu D. Shih L.M. Zee Y.C. J. Bacteriol. 1994; 176: 4761-4765Crossref PubMed Google Scholar). The reason for this extensive rRNA degradation is not yet understood. Starvation and stationary phases have in common a dramatic slowing or complete absence of growth. Consequently, other situations in which growth slows might also affect the stability of rRNA, and such is the case following a nutritional downshift. In a relaxed mutant Escherichia coli strain, a substantial portion of newly synthesized rRNA is degraded during the first 30 min after the downshift (15Molin S. von Meyenberg K. Maaloe O. Hansen M.T. Pato M.L. J. Bacteriol. 1977; 131: 7-17Crossref PubMed Google Scholar). Confirmation that growth rate affects stability comes from direct measurement of stable RNA accumulation in cells growing over a wide range of rates. At low growth rates, in particular, the balance between the synthesis of rRNA and ribosomal proteins is disturbed such that excess RNA is produced and ultimately degraded (16Norris T.E. Koch A.L. J. Mol. Biol. 1972; 64: 633-649Crossref PubMed Scopus (56) Google Scholar, 17Gausing K. J. Mol. Biol. 1977; 115: 335-354Crossref PubMed Scopus (136) Google Scholar). At very low growth rates as much as 70% of the newly synthesized rRNA does not accumulate in ribosomes and apparently is degraded. Moreover, some excess of rRNA over ribosomal protein may be synthesized at all growth rates (16Norris T.E. Koch A.L. J. Mol. Biol. 1972; 64: 633-649Crossref PubMed Scopus (56) Google Scholar, 17Gausing K. J. Mol. Biol. 1977; 115: 335-354Crossref PubMed Scopus (136) Google Scholar), suggesting that mechanisms must exist for removing the excess RNA because free rRNA does not accumulate (18Lindahl L. J. Mol. Biol. 1975; 92: 15-37Crossref PubMed Scopus (115) Google Scholar). Such quality control mechanisms will be discussed in more detail later. Some data suggest that at very slow growth rates a portion of newly made tRNA also may be degraded (16Norris T.E. Koch A.L. J. Mol. Biol. 1972; 64: 633-649Crossref PubMed Scopus (56) Google Scholar). However, this point has not been examined in detail. The breakdown of ribosomes and degradation of stable RNA under conditions of starvation, stationary phase, and slow growth would appear to be of major importance to bacterial cells under natural conditions. Enteric bacteria, such as E. coli, live under “feast or famine” conditions, and processes that release the stores of nutrients present in ribosomes would thus represent an important survival strategy. Understanding how this is accomplished and identifying the regulatory signals that underlie these degradative processes will be of considerable interest. Treatment of bacteria with any one of a variety of agents leads to extensive breakdown of cellular RNA, in some cases approaching the entire RNA content. Among the compounds promoting RNA degradation are antibiotics such as streptomycin (19Dubin D.T. J. Mol. Biol. 1964; 8: 749-767Crossref PubMed Scopus (14) Google Scholar), mitomycin C (20Suzuki H. J. Bacteriol. 1967; 94: 666-676Crossref PubMed Google Scholar), and polymixin E (21Nakajima K. Kawamata J. Biken J. 1966; 9: 115-123PubMed Google Scholar), membrane-damaging reagents such as toluene (22Jackson R.W. De Moss J.A. J. Bacteriol. 1965; 90: 1420-1425Crossref PubMed Google Scholar) and dodecyldiethanolamine (23Lambert P.A. Smith R.W. Microbios. 1976; 17: 35-49PubMed Google Scholar), and Hg2+ ion (24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar). A likely explanation for the action of many of these agents is an effect on the cell membrane leading to alterations in permeability. These changes affect the internal environment because of the loss of ions, including Mg2+, and as a consequence, ribosome structure may be altered, rendering the rRNA more accessible to the action of a degradative RNase. That this scenario probably is correct comes from evidence that RNA degradation in many of these situations is because of action of the nonspecific endoribonuclease, RNase I (21Nakajima K. Kawamata J. Biken J. 1966; 9: 115-123PubMed Google Scholar, 23Lambert P.A. Smith R.W. Microbios. 1976; 17: 35-49PubMed Google Scholar, 24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar). In cells lacking RNase I, the extensive RNA breakdown does not occur (23Lambert P.A. Smith R.W. Microbios. 1976; 17: 35-49PubMed Google Scholar, 24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar). Moreover, 3′-mononucleotides are among the degradation products (24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar), as expected for RNase I action. RNase I is thought to be present largely in the periplasmic space (25Neu H.C. Heppel L.A. J. Biol. Chem. 1964; 239: 3893-3900Abstract Full Text PDF PubMed Google Scholar), but membrane damage would allow entry of active RNase I into the cell. In addition, the loss of Mg2+, an inhibitor of RNase I, and the more exposed rRNA all combine to result in extensive RNA degradation. An interesting feature of the RNA breakdown induced by Hg2+ is that it occurs only in cells in exponential growth; cells in stationary phase are insensitive (24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar). It is thought that changes in the cell membrane, known to occur upon entry into stationary phase (25Neu H.C. Heppel L.A. J. Biol. Chem. 1964; 239: 3893-3900Abstract Full Text PDF PubMed Google Scholar), may affect the entry of RNase I into the cytoplasm. An additional feature of the Hg2+ ion activation of RNase I also needs to be considered. A portion of cellular RNase I resides in the cytoplasm, most likely in an inactive form (25Neu H.C. Heppel L.A. J. Biol. Chem. 1964; 239: 3893-3900Abstract Full Text PDF PubMed Google Scholar, 26Cannistraro V.J. Kennell D. J. Bacteriol. 1991; 173: 4653-4659Crossref PubMed Google Scholar). This raises the possibility that bacteria may contain a Hg2+ ion-sensitive inhibitor (24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar, L. T. J. Bacteriol. PubMed Google Scholar), as is known to be present in cells J. Biol. Chem. Full Text PDF PubMed Google Scholar). of the inhibitor would be on the of RNase evidence for such a bacterial RNase I inhibitor (24Beppu T. Arima K. J. Bacteriol. 1969; 98: 888-897Crossref PubMed Google Scholar, L. T. J. Bacteriol. PubMed Google Scholar), and by with would be an interesting by which the of RNase I be under physiological conditions. can a wide range of that would have the to affect RNA one of the mechanisms that must exist for stable RNAs cellular during exponential growth and for this when conditions RNA degradation. A with of rRNA or tRNA or ribosome ultimately leading to or RNAs that would to be A of an RNase and RNAs that would be such as with lacking RNase of these many of on the processes and that RNA and in fact, many studies these have been interesting mutant to rapidly rRNA and tRNA upon of RNA synthesis at Schlessinger D. Biol. 1972; PubMed Scopus Google Scholar). that the to a on the a membrane H. H. Biochem. Biophys. Res. 1977; PubMed Scopus Google Scholar). a consequence, RNase I, present in the the cytoplasm, and as leads to RNA degradation. conditions, the is and this is by a of or of degradation. the of this mutant how important it is for cells to active RNase I from the cytoplasm. for this must be because of RNase I by as much as has little effect on cell growth L. T. J. Bacteriol. PubMed Google Scholar). 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PubMed Scopus Google Scholar). discussed these cells accumulate large of of 16 and 23 S rRNA that normally would be degraded by the How the in the first has not yet been However, that rRNA may be synthesized in excess of ribosomal protein (16Norris T.E. Koch A.L. J. Mol. Biol. 1972; 64: 633-649Crossref PubMed Scopus (56) Google Scholar, 17Gausing K. J. Mol. Biol. 1977; 115: 335-354Crossref PubMed Scopus (136) Google Scholar) and that a certain of in rRNA synthesis or an of rRNA for of the is being The rRNA would likely be to the for by to the of ribosomal in fact, cells in which the rRNA are not ultimately lose viability S. A. PubMed Scopus Google Scholar). Thus, quality control of stable RNA metabolism would appear to be an important for cell at are known in E. coli and at in Mol. Biol. Rev. PubMed Scopus Google Scholar). However, although considerable has about the of these in mRNA decay and stable RNA relatively little about their in the degradation of stable RNA. 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Bacteriol. 1977; PubMed Google Scholar) and RNase is not RNase is a as it is known to be able to rRNA S. A. PubMed Scopus Google Scholar, J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar). RNase during starvation for other of nutrients as to be these are it may be that the of the stable RNA degradation have been importance to of stable RNA degradation is how these processes are In particular, one would to how RNA stability is during exponential growth and what are the signals and mechanisms that degradation in other The would be that RNAs are degraded they are the action of Thus, in growing the stability of rRNA would most likely be a of into ribosomes and by ribosomal It is known that synthesis of rRNA and of ribosomal proteins is over a range of growth rates (16Norris T.E. Koch A.L. J. Mol. Biol. 1972; 64: 633-649Crossref PubMed Scopus (56) Google Scholar, 17Gausing K. J. Mol. Biol. 1977; 115: 335-354Crossref PubMed Scopus (136) Google Scholar, L. J. Mol. Biol. 1975; 92: 15-37Crossref PubMed Scopus (115) Google Scholar). this is for by of rRNA J. Bacteriol. PubMed Google Scholar) or by more rapid synthesis with ribosomal proteins T. J. J. Mol. Biol. PubMed Scopus Google Scholar), the rRNA molecules become to degradation. Likewise, if an during ribosome that in of the rRNA, degradation also would but in this that would be to be a quality control S. A. PubMed Scopus Google Scholar). In the case of tRNA their to RNase action would from extensive and structure and from their with and The would be by In fact, when is or during the that a tRNA might be it can be on by RNase leading to of the A of the R. S. A. PubMed Scopus Google Scholar). Because RNase very at J. Biol. Chem. 2002; Full Text Full Text PDF PubMed Scopus Google Scholar), it would allowing for by tRNA This and of the of tRNA is the known tRNA Prog. Nucleic Acids Res. Mol. Biol. PubMed Scopus Google Scholar). of this for rRNA and tRNA stability during growth is that ribosomes and tRNA normally be to by cellular on of this is The one is when RNase I is present because ribosomes and tRNA are for this This would the for active RNase I in the from and the stable RNA degradation that occurs when RNase I does the as a of that damage the cell on these it is to how the cell would the periplasmic of RNase I for any such a large of RNase I to the cell in be the other activation of a of RNase I might be the to and what is for is the of stable RNA degradation under starvation conditions. the structure of the ribosome is to allow by certain or an RNase is The be accomplished by the of an RNase or by on an additional RNase in to the starvation Understanding how this is accomplished would be of considerable and may into RNA Likewise, identifying conclusively the for stable RNA degradation is of of bacterial and the of mutant lacking one or more of these such studies are to be the from such will it to the of stable RNA degradation to that of mRNA decay to the and between these