Weight-watching at the university: the consequences of growth.

We began by pointing out that tools (for example) have size optima that are dictated by function. If we assume that the university has a function, it would seem reasonable to think about the size which will serve that function best. The principle of size optimization is fundamental, but its application to the university at once encounters a difficulty: What is the function of a university? It might take forever to secure general agreement on the answer to this question. The problem is that universities have a number of different functions, to which different individuals will attach different weights, and each function may well have a unique size optimum. Just as it is, in general, mathematically impossible to maximize simultaneously for two different functions of the same variable (29), so it is unsound to conceive of a single optimum for the multiversity. Nonetheless, a range of workable sizes may be defined by analyzing the effect of variation in size on all essential functions. The examples from biological systems illustrate this approach. Cells exist in a variety of sizes, each size presumably representing an optimization to one or another set of constraints, yet there are upper bounds. There are no cells the size of basketballs because essential metabolic functions are limited by the surface-to-volume ratio. We must emphasize that one does not need a grand theory of life in order to identify this limiting condition. If cells could talk, they would no doubt differ on the general philosophy of being a cell, yet all conceptions would be subject to certain physically inevitable limitations on size. In the case of the university, no grand theory of education is needed in order to identify dysfunctions of growth that affect essential activities (for example, the diffusion of individuals through, in, and out of the university) or that affect all activities (for example, overall morale). Balanced against these dysfunctions are such advantages of growth as economy, the achievement of a critical mass, and flexibility in staffing. Our analyis of data from the California system indicates that unit costs of education decline very little above a size of 10,000 or 15,000 students. Moreover, the critical mass for departmental excellence, at least in terms of the ACE ratings of graduate departments, is achieved by a university of about this size. Growth beyond this size range conitinues to provide flexibility in staffing and spares administrators the trouble of having to make difficult decisions. At the same time, the dysfunctions attendant on growth become steadily more severe. Our impression is that the dysfunctions have not been seriously considered, while the advantages have been greatly oversold. The idea of dysfunctional growth, although fundamental in biology, contradicts one of America's most cherished illusions. Particular dysfunctions of growth are rarely formulated, set down, and explicitly weighed against the potential advantages. Rather, the American prejudice has been to assume that growth is always good, or at least inevitable, and to treat the dysfunctions (which are inevitable) as managerial problems to be ironed out later or glossed over. There has also been a remarkable failure to think in terms of optima and to distinguish in this way between what we have termed functional and dysfunctional growth. Rather, the tendency has been to extrapolate functional growth into the dysfunctional range: If a university population of 10,000 confers certain advantages as compared with a population of 1,000, then it is assumed that a population of 100,000 must confer even more advantages. We suggest that it is time, in fact past time, to subject university growth to a more searching scrutiny. Functional and dysfunctional consequences need to be spelled out. Scale effects ought to be considered in connection with every plan for expansion. Ideally, one might expect a farsighted and tough-minded administration to carry out this function. This has rarely been the case. Too often administrators regard their function as simply that of broker among competing expansionist tendencies. Such a conception replaces philosophy by politics and often encourages mindless growth. Perhaps it is time for faculties to involve themselves in long-range planning and to pay the price of a more satisfactory environment by giving up some individual dreams of empire. The first step for every large university ought to be a careful analysis of scale effects (30). If analysis indicates that continued growth of a university will be, on balance, dysfunctional, we suggest that plans be formulated to establish an absolute limit on further enrollment increase, and an absolute limit on further building expansion. If further analysis indicates that a university is already well into the dysfunctional size range, then the obvious solution is to cut back. If this turns out to be the case, then we suggest that a program for the gradual reduction of the campus population be undertaken. There are two distinct ways to accomplish this: (i) the establishment of a new university and (ii) the decentralization of the existing university into two or more campuses. Decentralization strikes us as an attractive idea, worthy of careful study. One of the recommendations of the Scranton commission was, "Large universities should take steps to decentralize or reorganize to make possible a more human scale" (18, p. 14). Returning to the natural world, we note again that cells do not grow indefinitely. Instead, they divide.

Leftward ribosome frameshifting at a hungry codon.

Previous experiments have shown that limitation for certain aminoacyl-tRNA species results in phenotypic suppression of a subset of frameshift mutant alleles, including members in both the (+) and (-) incorrect reading frames. Here, we demonstrate that such phenotypic suppression can occur through a ribosome reading frame shift at a hungry AAG codon calling for lysyl-tRNA in short supply. Direct amino acid sequence analysis of the product and DNA sequence manipulation of the gene demonstrate that the ribosome frameshift occurs through a movement of one base to the left, so as to decode the triplet overlapping the hungry codon from the left or 5' side, followed by continued normal translation in the new, shifted reading frame.

On the role of the P-site in leftward ribosome frameshifting at a hungry codon.

Previous work characterized ribosomal frameshifting within the sequence C UUC AAG provoked by lysyl-tRNA limitation. The ribosome frameshift is one base to the left of the AAG lysine codon, as shown by dotted overlining above. We now show that the frequency of this leftward ribosome frameshift is strongly influenced by the identity of the bases two, three and four positions to the left of the actual frameshift site. The nature of these influences coincides exactly with the possibilities of base-pairing between the sequence and the anticodon of the P-site peptidyl-tRNA when shifted one base to the left just upstream of the frameshift site. We conclude that a peptidyl shift in the P-site is intimately involved in leftward frameshifting in the adjacent A site when it codes for an aminoacyl-tRNA in short supply.

Frameshift suppression in aminoacyl-tRNA limited cells.

Under certain conditions aminoacyl-tRNA limitation can phenotypically suppress frameshift alleles. The observed suppression is due to an increase in abnormal translocation of ribosomes translating codons that have a short supply of aminoacyl-tRNA. The rIIB frameshift alleles of bacteriophage T4 are used here to pinpoint the sites of ribosome frameshifting caused by these hypothetical decoding errors. The data indicate that not all hungry codons are associated with abnormal translocation, only a relatively small subset. Analysis of the hungry codons which are associated with ribosome frameshifting points to the existence of severe context effects determining the shiftiness of these codons.

Uncharged tRNA error damping model.

Uncharged tRNA is known to bind to the ribosome in a codon-specific fashion. In this way, cognate uncharged tRNA competes with non-cognate aminoacyl-tRNA. If uncharged tRNA can be aminoacylated while on the ribosome, this will damp errors due to aminoacyl-tRNA imbalance. Kinetic analysis shows that this scheme reduces errors at 'hungry' codons considerably more effectively than J. Ninio's accuracy tuner model; for example, a 10-fold decrease in cognate aminoacyl-tRNA elicits only a 10% increase in the error frequency.

A model of clonal attenuation.

Two formal models of clonal attenuation [Kirkwood, T. B. L. & Holliday, R. (1975) J. Theor. Biol. 53, 481-496; Shall, S. & Stein, W. D. (1979) J. Theor. Biol. 76, 219-231] are considered in the light of recent data on the changing distribution of replicative potential among individual cultured fibroblasts on subcloning. The experimental data [Smith, J. R., Pereira-Smith, O. & Good, P. I. (1977) Mech. Ageing Dev. 6, 283-286] are shown to contradict both models. A new model, compatible with the subcloning data, is proposed. This model involves a gradual increase in the probability of commitment during cell growth in culture and a small number (about seven) of divisions following commitment. The gradual increase in commitment probability is shown to be compatible with the gradual accumulation of a gene product subject to autogenous regulation.

Bacillus subtilis relG mutant: defect in glucose uptake.

A previously described Bacillus subtilis mutant which exhibits a relaxed phenotype after glucose limitation (relG) has been characterized further. Analysis of this mutant and of the downshift mechanism in B. subtilis has shown that the primary defect lies in glucose uptake.

The glucose effect in Bacillus subtilis.

An analysis of the glucose downshift mechanism in Bacillus subtilis has shown that the depression of catabolic enzymes characteristic of the 'glucose effect' includes isocitrate dehydrogenase and glucose-6-phosphate dehydrogenase. Additionally, phosphofructokinase undergoes what appears to be a reversible modification regulated by glucose transport.

The role of RNA polymerase in transcriptional fidelity.

The overall transcription of DNA has previously been demonstrated to proceed at extremely high levels of accuracy. We review the evidence that the process of transcription is subject to proof-reading in the Hopfield sense. In addition, we speculate that the proof-reading activity associated with transcription is subject to cyclical phase transitions. That is, during periods of low processivity associated with initiation, RNA synthesis is relatively imprecise. The transition to the elongation phase of RNA synthesis, characterized by a shift to high processivity, is accompanied by enhanced proof-reading. A model for the damping of transcriptional errors, based on a PPi-mediated processive pyrophosphorolysis reaction, is discussed in terms of pausing during transcription.

Ribosomes can slide over and beyond "hungry" codons, resuming protein chain elongation many nucleotides downstream.

In cells subjected to moderate aminoacyl-tRNA limitation, the peptidyl-tRNA-ribosome complex stalled at the "hungry" codon can slide well beyond it on the messenger RNA and resume translation further downstream. This behavior is proved by unequivocal amino acid sequence data, showing a protein that lacks the bypassed sequence encoded between the hungry codon and specific landing sites. The landing sites are codons cognate to the anticodon of the peptidyl-tRNA. The efficiency of this behavior can be as high as 10-20% but declines with the length of the slide. Interposition of "trap" sites (nonproductive landing sites) in the bypassed region reduces the frequency of successful slides, confirming that the ribosome-peptidyl-tRNA complex passes through the untranslated region of the message. This behavior appears to be quite general: it can occur at the two kinds of hungry codons tested, AUA and AAG; the sliding peptidyl-tRNA can be any of three species tested, phenylalanine, tyrosine, or leucine tRNA; the peptidyl component can be either of two very different peptide sequences; and translation can resume at any of the three codons tested.

Phosphorolytic error correction during transcription.

Escherichia coli DNA-directed RNA polymerase is shown to contain a novel phosphorolytic error correction activity which removes erroneous nucleotides, as rNDPs, from the 3'-end of the growing transcript. The activity we describe is biochemically similar to polynucleotide phosphorylase (PNP), yet in contrast to PNP is activated by Mn2+. We demonstrate that the activity, which is mediated by Pi, is dependent on the presence of an incorrectly incorporated nucleotide at the leading 3'-end of the transcript. The correction activity we describe exhibits a 4 x 10(4)-fold preference for the excision of incorrect nucleotides from the transcript. These findings suggest the possibility that RNA phosphorolysis may play a critical role in the process of transcriptional proofreading.

A new relaxed mutant of Bacillus subtilis.

A new relaxed mutant of Bacillus subtilis was isolated by screening Rifr clones for alterations in stringent control. The Rifr relaxed mutant which is described was found to contain a second-site mutation conferring a relaxed response to an energy source downshift and was partially relaxed after amino acid starvation. The new rel locus, called relG, was distinct from the two other known rel loci in B. subtilis, relA, and relC.

Context rules of rightward overlapping reading.

We have investigated the mechanism and sequence context rules governing ribosome frameshifting promoted by aminoacyl-tRNA limitation. In the case of one shifty sequence, frameshifting promoted by lysyl-tRNA limitation occurs at the sequence AAG C and is due to rightward movement of the ribosome so as to read the AGC triplet overlapping the hungry codon from the right. The frequency of this event is unaffected by sequence elements more than three bases to the left (upstream) or two bases to the right (downstream) of the hungry codon, and only slightly affected by the identity of the base two bases to the right. It is strongly affected by the base immediately to the right of the hungry codon, which becomes the wobble base of the shifted triplet; and by the third base of the hungry codon, even though the two synonyms (AAG and AAA) call for the same aminoacyl-tRNA; and by the identity of the base immediately to the left of the hungry codon. The latter result suggests that the aminoacyl-tRNA in the P site affects the maintenance of reading frame at the adjacent A site of the ribosome. However, the DNA sequence makes it seem unlikely that the P-site tRNA shifts to the right in concert with the A-site tRNA, a mechanism that can account for leftward frameshifting (in the opposite direction) in retroviral translation. The specificity of sequence determinants of leftwing versus rightwing frameshifting is discussed.

Regulation of ribosomal and transfer RNA synthesis by guanosine 5'-diphosphate-3'-monophosphate.

Permeabilized cells of Escherichia coli were used to examine the effect on RNA synthesis of guanosine 5'-diphosphate-3'-monophosphate (ppGp). Electrophoretic and hybridization analysis of bulk RNA demonstrated that ppGp selectively reduced the accumulation of both ribosomal and transfer RNAs. The experiments further suggested that the observed reduction in stable RNA accumulation resulted from a reduction in stable RNA chain initiation rather than an effect on elongation, processing, or maturation of stable RNA transcripts. In contrast, the expression of the lac Z gene was not affected by ppGp. These results suggest that ppG, a nucleotide produced in E. coli during the stringent response, could play a direct role in the stringent regulation of stable RNA synthesis.