Stability of the cellular translation process

The Many Roles Mitochondria Play in Mammalian Aging

Significance: Aging is a natural process that affects most living organisms, resulting in increased mortality. As the world population ages, the prevalence of age-associated diseases, and their associated health care costs, has increased sharply. A better understanding of the molecular mechanisms that lead to cellular dysfunction may provide important targets for interventions to prevent or treat these diseases. Recent Advances: Although the mitochondrial theory of aging had been proposed more than 40 years ago, recent new data have given stronger support for a central role for mitochondrial dysfunction in several pathways that are deregulated during normal aging and age-associated disease. Critical Issues: Several of the experimental evidence linking mitochondrial alterations to age-associated loss of function are correlative and mechanistic insights are still elusive. Here, we review how mitochondrial dysfunction may be involved in many of the known hallmarks of aging, and how these pathways interact in an intricate net of molecular relationships. Future Directions: As it has become clear that mitochondrial dysfunction plays causative roles in normal aging and age-associated diseases, it is necessary to better define the molecular interactions and the temporal and causal relationship between these changes and the relevant phenotypes seen during the aging process. Antioxid. Redox Signal. 36, 824-843.

Hematopoietic stem cell regulation by the proteostasis network

PURPOSE OF REVIEW

Protein homeostasis (proteostasis) is maintained by an integrated network of physiological mechanisms and stress response pathways that regulate the content and quality of the proteome. Maintenance of cellular proteostasis is key to ensuring normal development, resistance to environmental stress, coping with infection, and promoting healthy aging and lifespan. Recent studies have revealed that several proteostasis mechanisms can function in a cell-type-specific manner within hematopoietic stem cells (HSCs). Here, we review recent studies demonstrating that the proteostasis network functions uniquely in HSCs to promote their maintenance and regenerative function.

RECENT FINDINGS

The proteostasis network is regulated differently in HSCs as compared with restricted hematopoietic progenitors. Disruptions in proteostasis are particularly detrimental to HSC maintenance and function. These findings suggest that multiple aspects of cellular physiology are uniquely regulated in HSCs to maintain proteostasis, and that precise control of proteostasis is particularly important to support life-long HSC maintenance and regenerative function.

SUMMARY

The proteostasis network is uniquely configured within HSCs to promote their longevity and hematopoietic function. Future work uncovering cell-type-specific differences in proteostasis network configuration, integration, and function will be essential for understanding how HSCs function during homeostasis, in response to stress, and in disease.

The intersection of exercise and aging on mitochondrial protein quality control

Skeletal muscle quality and quantity are negatively impacted with age. Part of this decline in function can be attributed to alterations in mitochondrial turnover, and in the mechanisms that regulate mitochondrial homeostasis. Protein quality control within the mitochondria relies on a number of interconnected processes, namely the mitochondrial unfolded protein response (UPR^mt), protein import and mitophagy. In particular, the post-transcriptional regulation of protein import into the organelle has generated considerable recent interest in view of its dynamic versatility. The capacity for import can be increased by chronic exercise, and diminished by muscle disuse, and defects in the import pathway can be rescued by exercise. Within mitochondria, the unfolded protein response (UPR) is activated if protein import is altered, or if protein misfolding takes place. This UPR generates retrograde signaling to the nucleus to activate compensatory gene expression and protein synthesis. Mitophagy is also elevated with age, contributing to the lower mitochondrial content in aging muscle. However, mitophagy is amenable to exercise adaptations, as it is activated with each exercise bout, presumably to mediate mitochondrial quality control. However, this response is attenuated in older subjects. Although not yet completely elucidated, numerous molecular processes involved in mitochondrial biogenesis and turnover are affected with age. The contrasting and often opposite consequences of exercise and age suggest that exercise can serve as non-pharmacological "mitochondrial medicine" for aging muscle to ameliorate mitochondrial content and function, via pathways that implicate organelle protein quality control mechanisms.

Biogerontology: research status, challenges and opportunities

Biogerontology is the study of the biological basis of ageing and age-related diseases. The phenomenon and the process of ageing are well understood in evolutionary and biological terms; and a conceptual framework has been established within which general principles of ageing and longevity can be formulated. The phenotype of ageing in terms of progressive loss of physical function and fitness is best seen during the period of survival after the evolution-determined essential lifespan (ELS) of a species. However, the ageing phenotype is highly heterogenous and individualistic at all levels from the whole body to the molecular one. Most significantly, the process and the progression of ageing are not determined by any specific gerontogenes. Ageing is the result of imperfect maintenance and repair systems that allow a progressive shrinkage of the homeodynamic space of an individual. The challenge is to develop and apply wholistic approaches to the complex trait of ageing for maintaining and/or improving health. One such approach is that of mild stress-induced physiological hormesis by physical, mental and nutritional hormetins. Biogerontological research offers numerous opportunities for developing evidence-based novel biomedical technologies for maintaining and improving health, for preventing the onset of age-related diseases, and for extending the health-span.

mTOR signaling in protein homeostasis: less is more?

A proper balance between synthesis, maturation and degradation of cellular proteins is crucial for cells to maintain physiological functions. The costly process of protein synthesis is tightly coupled to energy status and nutrient levels by the mammalian target of rapamycin (mTOR), whereas the quality of newly synthesized polypeptides is largely maintained by molecular chaperones and the ubiquitin-proteasome system. There is a wealth of evidence indicating close ties between the nutrient signaling pathway and the intracellular stress response. Dysregulation of both systems has been implicated in aging and age-associated pathologies. In this review, we describe molecular mechanisms underlying the connection between mTOR and the chaperone network and discuss the importance of their functional interaction in growth and aging.

Mitochondrial protein quality control during biogenesis and aging

Mitochondrial dysfunction has long been associated with the aging process and the onset of numerous diseases. Regulation of the complex protein-folding environment within the organelle is essential for maintaining efficient metabolic output. Over time, dysregulation of protein homeostasis arises through stress induced by the accumulation of reactive oxygen species and mutations in the mitochondrial genome introduced during replication. To preserve organelle function during biogenesis, remodeling and stress, quality control of mitochondrial proteins must be monitored by molecular chaperones and proteases stationed in the four compartments of the organelle. Here, we review mitochondrial protein quality control with a focus on organelle biogenesis and aging.

Error-protein metabolism and ageing

Ageing and many associated pathologies are accompanied by accumulation of altered proteins. It is suggested that erroneous polypeptide biosynthesis, cytosolic and mitochondrial, is not an insignificant source of aberrant protein in growing and non-mitotic cells. It is proposed that (i) synthesis of sufficient proteases and chaperone proteins necessary for rapid elimination of altered proteins, from cytoplasmic and mitochondrial compartments, is related to cellular protein biosynthetic potential, and (ii) cells growing slowly, or not at all, automatically generate lower levels of protease/chaperone molecules than cells growing rapidly, due to decreased general rate of protein synthesis and lowered amount of error-protein produced per cell. Hence the increased vulnerability of mature organisms may be explained, at least in part, by the decline in constitutive protease/chaperone protein biosynthesis. Upregulation of mitochondria biogenesis, induced by dietary restriction or aerobic exercise, may also increase protease/chaperone protein synthesis, which would improve cellular ability to degrade both error-proteins and proteins damaged post-synthetically by reactive oxygen species etc. These proposals may help explain, in part, the latency of those age-related pathologies where altered proteins accumulate only late in life, and the beneficial effects of aerobic exercise and dietary restriction.

On methionine restriction, suppression of mitochondrial dysfunction and aging

Rats and mice, when subjected to methionine restriction (MetR), may live longer with beneficial changes to their mitochondria. Most explanations of these observations have centered on MetR somehow suppressing the effects of oxygen free radicals. It is suggested here that MetR's effects on protein metabolism should also be considered when attempting to explain its apparent anti-aging actions. Methionine is the initiating amino acid in mRNA translation. It is proposed that MetR decreases the protein biosynthesis rate due to methionine limitation, which correspondingly decreases generation of ribosomal-mediated error proteins, which then lowers the total abnormal protein load that cellular proteases and chaperone proteins (mitochondrial and cytoplasmic) must deal with. This will increase protease availability for elimination of proteins damaged postsynthetically and help delay abnormal protein accumulation, the major molecular symptom of aging. The slowed rate of protein synthesis may also alter protein folding, which could also alter polypeptide susceptibility to oxidative attack. MetR will also increase lysosomal proteolysis, including autophagy of dysfunctional mitochondria, and promote mitogenesis. MetR may decrease synthesis of S-adenosyl-methionine (SAM), which could decrease spontaneous O(6)-methylguanine formation in DNA. However decreased SAM may compromise repair of protein isoaspartate residues by protein-isoaspartate methyltransferase (PIMT). Changes in SAM levels may also affect gene silencing. All the above may help explain, at least in part, the beneficial effects of MetR.

On why decreasing protein synthesis can increase lifespan

An explanation is offered for the increased lifespan of Caenorhabditis elegans when mRNA translation is inhibited due to loss of the initiation factor IFE-2 [Hansen, M., Taubert, T., Crawford, D., Libina, N., Lee, S.-J., Kenyon, C., 2007. Lifespan extension by conditions that inhibit translation in Caenorhabditis elegans. Ageing Cell 6, 95-110; Pan, K.Z., Palter, J.E., Rogers, A.N., Olsen, A., Chen, D., Lithgow, G.J., Kapahi, P., 2007. Inhibition of mRNA translation extends lifespan in Caenorhabditis elegans. Ageing Cell 6, 111-119; Syntichaki, P., Troulinaki, K., Tavernarakis, N., 2007. eIF4E function in somatic cells modulates ageing in Caenorhabditis elegans. Nature 445, 922-926]. It is suggested that the general reduction of protein synthesis, due to the decreased frequency of mRNA translation, also lowers the cellular load of erroneously synthesized polypeptides which the constitutive protein homeostatic apparatus (proteases and chaperones proteins) normally eliminates. This situation results in "spare" proteolytic and chaperone function which can then deal with those proteins modified post-synthetically, e.g. by oxidation and/or glycation, which are thought to contribute to the senescent phenotype. This increased availability of proteolytic and chaperone functions may thereby contribute to the observed increase in organism stress resistance and lifespan.

Complex signals in the genomic 3' nontranslated region of bovine viral diarrhea virus coordinate translation and replication of the viral RNA

The genomes of positive-strand RNA viruses strongly resemble cellular mRNAs. However, besides operating as a messenger to generate the virus-encoded proteins, the viral RNA serves also as a template during replication. A central issue of the viral life cycle, the coordination of protein and RNA synthesis, is yet poorly understood. Examining bovine viral diarrhea virus (BVDV), we report here on the role of the variable 3'V portion of the viral 3' nontranslated region (3'NTR). Genetic studies and structure probing revealed that 3'V represents a complex RNA motif that is composed of synergistically acting sequence and structure elements. Correct formation of the 3'V motif was shown to be an important determinant of the viral RNA replication process. Most interestingly, we found that a proper conformation of 3'V is required for accurate termination of translation at the stop-codon of the viral open reading frame and that efficient termination of translation is essential for efficient replication of the viral RNA. Within the viral 3'NTR, the complex 3'V motif constitutes also the binding site of recently characterized cellular host factors, the so-called NFAR proteins. Considering that the NFAR proteins associate also with the 5'NTR of the BVDV genome, we propose a model where the viral 3'NTR has a bipartite functional organization: The conserved 3' portion (3'C) is part of the nascent replication complex; the variable 5' portion (3'V) is involved in the coordination of the viral translation and replication. Our data suggest the accuracy of translation termination as a sophisticated device determining viral adaptation to the host.

Diversity in the rates of transcript elongation by single RNA polymerase molecules

Single-molecule measurements of the activities of a variety of enzymes show that rates of catalysis may vary markedly between different molecules in putatively homogeneous enzyme preparations. We measured the rate at which purified Escherichia coli RNA polymerase moves along a approximately 2650-bp DNA during transcript elongation in vitro at 0.5 mm nucleoside triphosphates. Individual molecules of a specifically biotinated RNA polymerase derivative were tagged with 199-nm diameter avidin-coated polystyrene beads; enzyme movement along a surface-linked DNA molecule was monitored by observing changes in bead Brownian motion by light microscopy. The DNA was derived from a naturally occurring transcription unit and was selected for the absence of regulatory sequences that induce lengthy pausing or termination of transcription. With rare exceptions, individual enzyme molecules moved at a constant velocity throughout the transcription reaction; the distribution of velocities across a population of 140 molecules was unimodal and was well fit by a Gaussian. However, the width of the Gaussian, sigma = 6.7 bp/s, was considerably larger than the precision of the velocity measurement (1 bp/s). The observations show that different transcription complexes have differences in catalytic rate (and thus differences in structure) that persist for thousands of catalytic turnovers. These differences may provide a parsimonious explanation for the complex transcription kinetics observed in bulk solution.

Twenty years of ageing research at the Mill Hill laboratories

Research on ageing was carried out in the Genetics Division laboratories, Mill Hill, London, from 1970 to 1990, resulting in more than 100 publications. The work centred around the in vitro ageing of human diploid fibroblasts, but there was also research on transformed cells, rat and mouse tissues, human lymphocytes, chick cells, mice and a microbial model system. The major conclusion from all this research, together with a broad overview of the whole field of gerontology, is that ageing has multiple causes, and that adult animals become senescent through the eventual failure of several important maintenance mechanisms.

Expression of mutant alanine tRNAs increases spontaneous mutagenesis in Escherichia coli

The expression of mutA, an allele of the glycine tRNA gene glyV, can confer a novel mutator phenotype that correlates with its ability to promote Asp-->Gly mistranslation. Both activities are mediated by a single base change within the anticodon such that the mutant tRNA can decode aspartate codons (GAC/U) instead of the normal glycine codons (GCC/U). Here, we investigate whether specific Asp-->Gly mistranslation is required for the unexpected mutator phenotype. To address this question, we created and expressed 18 individual alleles of alaV, the gene encoding an alanine tRNA, in which the alanine anticodon was replaced with those specifying other amino acids such that the mutant (alaVX) tRNAs are expected to potentiate X-->Ala mistranslation, where X is one of the other amino acids. Almost all alaVX alleles proved to be mutators in an assay that measured the frequency of rifampicin-resistant mutants, with one allele (alaVGlu) being a stronger mutator than mutA. The alaVGlu mutator phenotype resembles that of mutA in mutational specificity (predominantly transversions), as well as SOS independence, but in a puzzling twist differs from mutA in that it does not require a functional recA gene. Our results suggest that general mistranslation (as opposed to Asp-->Gly alone) can induce a mutator phenotype. Furthermore, these findings predict that a large number of conditions that increase translational errors, such as genetic defects in the translational apparatus, as well as environmental and physiological stimuli (such as amino acid starvation or exposure to antibiotics) are likely to activate a mutator response. Thus, both genetic and epigenetic mechanisms can accelerate the acquisition of mutations.

Evolution: the dialogue between life and death

Organisms have the ability to harness energy from the environment to create order and to reproduce. From early error-prone systems natural selection acted to produce present day organisms with high accuracy in the synthesis of macromolecules. The environment imposes strict limits on reproduction, so evolution is always accompanied by the discarding of a large proportion of the less fit cells, or organisms. Sexual reproduction depends on an immortal germline and a soma which may be immortal or mortal. Higher animals living in hazardous environments have evolved aging and death of the soma for the benefit of the ongoing germline.

The evolutionary design of error-rates, and the fast fixation enigma

Genetic and non-genetic error-rates are analyzed in parallel for a lower and a higher organism (E. coli and man, respectively). From the comparison of mutation with fixation rates, contrasting proposals are made, concerning the arrangement of error-rates in the two organisms. In E. coli, reproduction is very conservative, but genetic variability is high within populations. Most mutations are discarded by selection, yet single mutational variants of a gene have, on average, little impact on fitness. In man, the mutation rate per generation is high, the variability generated in the population is comparatively low, and most mutations are fixed by drift rather than selection. The variants of a gene are in general more deleterious than in E. coli. There is a discrepancy in the published mutation rates: the rate of mutation fixations in human populations is twice or four times higher than the individual rate of mutation production, a feature which is not consistent with current population genetics models. Two, not mutually exclusive, hypotheses may explain this 'fast fixation enigma': (i) Mutation rates have substantially decreased in recent human evolution and (ii) A substantial fraction of the fixed mutations were generated in a process-such as gene conversion-that violates the principle of independence of mutation events.

Mutants in the Exo I motif of Escherichia coli dnaQ: defective proofreading and inviability due to error catastrophe

The Escherichia coli dnaQ gene encodes the proofreading 3' exonuclease (epsilon subunit) of DNA polymerase III holoenzyme and is a critical determinant of chromosomal replication fidelity. We constructed by site-specific mutagenesis a mutant, dnaQ926, by changing two conserved amino acid residues (Asp-12-->Ala and Glu-14-->Ala) in the Exo I motif, which, by analogy to other proofreading exonucleases, is essential for the catalytic activity. When residing on a plasmid, dnaQ926 confers a strong, dominant mutator phenotype, suggesting that the protein, although deficient in exonuclease activity, still binds to the polymerase subunit (alpha subunit or dnaE gene product). When dnaQ926 was transferred to the chromosome, replacing the wild-type gene, the cells became inviable. However, viable dnaQ926 strains could be obtained if they contained one of the dnaE alleles previously characterized in our laboratory as antimutator alleles or if it carried a multicopy plasmid containing the E. coli mutL+ gene. These results suggest that loss of proofreading exonuclease activity in dnaQ926 is lethal due to excessive error rates (error catastrophe). Error catastrophe results from both the loss of proofreading and the subsequent saturation of DNA mismatch repair. The probability of lethality by excessive mutation is supported by calculations estimating the number of inactivating mutations in essential genes per chromosome replication.

Connections between translation, transcription and replication error-rates

The analysis of published data from E coli suggests that in all three processes of translation, transcription, and replication, a minority of errors are produced by sub-classes of error-prone components. These add to the basal level of errors a noise of about 10 to 30%. Each one of the three processes contributes to the noisiness of the two others in a loose manner: a large increase in one error-rate produces a moderate increase in another error-rate. The strongest influence is that of transcription on translation errors. There it is possible that a majority of the misacylation errors are produced during the encounter of a correct amino acyl-tRNA ligase with a mistranscribed tRNA. Extreme mutator mutants are expected to produce a moderate increase in translation errors.

Four letters in the genetic alphabet: a frozen evolutionary optimum?

Piccirilli et al. (Nature, Lond. 343, 33-37 (1990)) have shown experimentally that the replicatable introduction of new base pairs into the genetic alphabet is chemically feasible. The fact that our current genetic alphabet uses only two base pairs can be explained provided that this basic feature of organisms became fixed in an RNA world utilizing ribozymes rather than protein enzymes. The fitness of such ribo-organisms is determined by two factors: replication fidelity and overall catalytic efficiency (basic metabolic or growth rate). Replication fidelity is shown to decrease roughly exponentially, and catalytic efficiency is shown to increase with diminishing returns, with the number of letters for a fixed genome length; hence their product, i.e. fitness, gives rise to a set of values with an optimum. Under a wide range of parameter values the optimum rests at two base pairs. The chemical identity of the particular choice in our genetic alphabet can also be rationalized. This optimum is considered frozen, as currently the dominant catalysts are proteins rather than RNAs.

Amino acid misincorporation during high-level expression of mouse epidermal growth factor in Escherichia coli

To determine whether the high-level expression of foreign proteins in Escherichia coli can lead to frequent translational errors, we analyzed amino acid misincorporation in mouse epidermal growth factor (mEGF) produced as a TrpE fusion protein. The mEGF DNA does not encode phenylalanine and determining the phenylalanine content of the purified protein will measure missense errors. Using this approach, we found an error frequency of about 1 in 40 for codons differing by a single base from those for phenylalanine. This is at least ten times higher than the error rate found for normal E. coli protein synthesis and may be due to limiting supply of charged tRNAs and GTP, brought about by the high-level production of the heterologous protein. The unexpectedly high error rate has implications for the clinical use of E. coli-derived therapeutic proteins.

Senescence and the accumulation of abnormal proteins

Mammalian cells can produce abnormal proteins in a number of different ways. These include random errors during protein synthesis, spontaneous or metabolite-induced modifications of amino acid sidechains and changes in polypeptide folding. The evidence that such alterations occur in proteins during growth and senescence is discussed. An important function controlling the accumulation of abnormal proteins is the rate at which they are hydrolysed by proteases. Modified proteins are much better protease substrates than their normal parent molecules, but in spite of this sensitivity to proteolysis they accumulate during ageing. This indicates a drop during senescence in the activity of those proteases degrading abnormal polypeptides. Ways in which abnormal proteins could inhibit cell growth and how these inhibitions may be negated during the immortalisation of diploid cells are discussed.

Protein synthesis and the components of protein synthetic machinery during cellular aging

The slowing down of protein synthesis is a change widely observed during the aging of organisms. It has also been claimed that a decline in the rate of protein synthesis occurs during cellular aging. However, the evidence in favour of this view is not clear-cut, and reliable estimates of rates of protein synthesis during cellular aging have yet to be made. Studies on various components of the protein synthetic machinery during cellular aging have revealed a decline in the efficiency and accuracy of ribosomes, an increase in the levels of rRNA and tRNA, and a decrease in the amounts and activities of elongation factors. Detailed studies on the structure and function of ribosomes, tRNA isoacceptor profiles, activities of aminoacyl-tRNA synthetases, levels and activities of initiation factors, rates of protein elongation, and the accuracy of protein synthesis will be needed before the molecular mechanisms of the regulation of protein synthesis during cellular aging can be understood.

Mechanisms responsible for the limited lifespan and immortal phenotypes in cultured mammalian cells

Normal mammalian cells have a limited lifespan in culture and hypotheses explaining cellular senescence usually fall into one of two categories. One of these postulates that random errors or damage accumulate in essential macromolecules and eventually outstrip the cell's capacity for resynthesis and repair. The second considers the changes when immortal clones are produced from normal cells and in particular the lifespans of hybrids when cells of differing growth potentials are fused. These data can be explained by postulating that the mortal phenotype is dominant and that trans-acting growth inhibitors are involved in limiting lifespan. But the results do not indicate if the inhibitors are the primary cause of senescence or a secondary effect induced by quite different initial events. We suggest that normal cells possess proof-reading mechanisms which monitor the accuracy of chromosome segregation and replication and which can induce the synthesis of growth inhibitors when they detect major errors in chromosome metabolism. It is further postulated that random damage accumulates during the growth of normal cells and eventually leads to detectable chromosome changes and the synthesis of inhibitors. Our hypothesis predicts that the emergence of immortal clones will be linked to the absence of active inhibitors and therefore to a loss in the fidelity of chromosome metabolism. Data are quoted which show that in contrast to normal cells, immortal clones have highly irregular karyotypes, amplify segments of their chromosomes, integrate exogenous DNA efficiently, maintain a constant level of 5-methylcytosine residues and have high frequencies of chromosomal aberrations. The mechanism of the proof-reading is unknown, but it may monitor changes in the patterns by which chromosome domains are attached to the nuclear matrix.

Changes in protein turnover after heat shock are related to accumulation of abnormal proteins in aging Drosophila melanogaster

Adult Drosophila melanogaster kept at 24 degrees C show a progressive decline in the synthesis and degradation of proteins with age. After exposure of young, 7-10 days old flies to 20 min of heat shock at 37 degrees C, the incorporation of [35S]-methionine into trichloroacetic acid precipitable proteins decreases to more than 60% of that observed in non-stressed flies. This decrease is also accompanied by a lower protein degradation rate. In contrast, the same stress in old, 49 days old insects results in a 3-fold increase in protein synthesis as compared to either non-heat shocked senescent flies or to young heat-shocked flies. The older flies also have faster protein turnover than unshocked controls. An effect similar to that observed in senescent Drosophila also occurs in young flies that have been fed canavanine, an arginine analogue, before and during heat shock. These results suggest that an age dependent accumulation of abnormal proteins may be responsible for the changes in protein turnover observed in the heat-shocked old flies.

Identification of minor tightly bound H1 histone subfractions which fail to cleave their initiator methionine

Groups of CBA mice were administered [35S] methionine (1 mCi/mouse). Non-histone proteins, H1 and H1(0) histones and nucleosomal core histones were isolated from different issues by selective extractions. The measurements of radioactivity of individual bands and autoradiography of dry gels were used to identify methionine-containing and methionine-free histone variants. H1A and H1B histone variants extracted with 5% perchloric acid were methionine-free. However, minor sub-fractions of these histones which are more tightly bound to DNA (and which can be extracted only with 0.25 N HCl) contained [35S] methionine and did show a higher specific activity than methionine-containing nucleosomal hitones. Cyanogen Bromide reaction which destroys non-histone proteins and methionine-containing nucleosomal histones removes radioactivity but does not alter the position of methionine-containing H1 minor bands. This indicates that the radioactive methionine occupies only the N-terminus of the H1 molecules. It is suggested that this methionine is an uncleaved initiator methionine. The presence of these methionine-containing minor H1 subfractions varies in different tissues.

DNA, mutations and aging

Genetic instability is widely thought to be involved in the process of aging. Evolutionary theory suggests that aging may well result from stochastic damage to DNA. However, studies of the dynamics of accumulation of simple somatic mutations have shown that such a mechanism cannot readily account for experimental observations. A more complex mutational theory of aging is emerging which allows for interaction between mutations, for damage to epigenetic controls on gene expression, and for interaction of (epi)genetic changes with other possible molecular events contributing to aging.

Decreased accuracy of protein synthesis in extracts from aging human diploid fibroblasts

The accuracy of protein synthesis has been measured in extracts from human diploid fibroblasts of different ages. Extracts were supplied with purified mRNA for the coat protein of the cowpea variant of tobacco mosaic virus (CcTMV), which lacks codons for cysteine and methionine. The presence of 35S-cysteine in CcTMV coat protein synthesized during translation reactions therefore represents translational error. Translation reactions were performed with extracts from young fibroblasts (less than 50% of life span completed) and old fibroblasts (more than 90% of life span completed), and the translation products were purified by immunoprecipitation and analyzed by polyacrylamide gel electrophoresis. The error frequency increased from 4.2 x 10(-5) cysteines/amino acid in young cell extracts to 2.9 x 10(-4) cysteines/amino acid in old cell extracts. Cysteine incorporation was not due to nonspecific binding, and could be increased approximately sixfold by the addition of the misreading antibiotic, paromomycin. It is concluded that translational accuracy is not stable during aging in vitro, and it is proposed that this decrease in the fidelity of information transfer could be responsible for the variety of changes observed in aging cultured human cells.

Age related reactivation of an X-linked gene

We have investigated age-related reactivation of the X chromosome by devising a model in which reactivation of a single gene in one cell among many can be identified. We have used mice with an X-autosomal translocation giving consistent non-random inactivation of the normal X (as judged by biochemical and cytogenetic techniques), that also carry a defective form of a histochemically demonstrable X-linked enzyme. When the gene for the normal enzyme was located on the inactivated normal X a uniformly negative histochemical picture would be predicted in doubly heterozygous animals. A very small proportion of enzyme-positive cells was found in young animals. This proportion increased very significantly with age, but the patch size did not change, showing that the result was not due to preferential division of enzyme-positive cells, but was instead due to the conversion of previously enzyme-negative to enzyme-positive cells. These observations provide the first evidence with a true X-linked gene for an age-related decrease in the stability of the X-inactivation mechanism.

Theoretical modelling of protein synthesis

This article provides an overview of the use of mathematical and computer modelling in furthering the understanding of protein synthesis. In particular, we discuss issues such as the nature of the rate limiting step(s), error rates, tRNA-codon adaptation, codon bias, attenuation control, and problems of selection and error corrections, focussing on their theoretical treatment.

Does streptomycin cause an error catastrophe?

We have examined the interpretation that streptomycin kills a bacterial culture by initiating the so-called error catastrophe. In particular, we asked whether the increased translational error rate induced by the antibiotic gives rise to an autocatalytic loss of functional fidelity of the devices responsible for gene expression, which ultimately causes the death of the culture. We have analyzed the performance characteristics of one of these devices, namely the ribosome in streptomycin-treated bacteria. We find that, although the treated ribosomes are constructed from error-containing proteins, they are not significantly different in elongation rate and fidelity from those ribosomes taken from untreated bacteria. We conclude that the bacteriocidal effect of streptomycin is not due to the initiation of an error catastrophe.

Strong effects of 5-azacytidine on the in vitro lifespan of human diploid fibroblasts

Azacytidine (5-aza-CR) and azadeoxycytidine (5-aza-CdR) are known to inhibit the methylation of cytosine (5-mC) in DNA, and their effects on the long-term growth of human fibroblasts, strain MRC-5, have been examined. A single treatment with either analogue initially inhibits growth, but the cells recover to normal morphology, growth rate and cell density at confluence. However, a memory of the treatment is retained, since the cells' subsequent lifespan is considerably reduced in comparison with controls, and the terminal stages of growth are indistinguishable from senescent cultures of untreated cells. The effect of 5-aza-CR or 5-aza-CdR does not appear to be closely related to the concentration used, or to the length of treatment up to about half-way through the total lifespan. Sequential doses have cumulative effects on longevity. There is evidence that the pattern of 5-mC in mammalian DNA is inherited via cell division; therefore, a reduction in 5-mC induced by a pulse treatment of 5-aza-CR or 5-aza-CdR will be transmitted to all descendants. The results are consistent with independent observations that the level of 5-mC declines continually during the serial subculture of human diploid cells. The analogues would be expected to precipitate this decline and thereby advance the physiological age of the culture. The results provide support for the view that the random loss of methyl groups in DNA may eventually have deleterious consequences, such as aberrant epigenetic changes in gene expression.

Scrapie, ribosomal proteins and biological information

Consideration of the autocatalytic synthesis of ribosomal proteins leads to a criterion for the infectivity of a foreign proteinaceous species in terms of the biochemical rate constants governing the propagation of errors during the translation of genetic information in a model system. Evidence pertaining to the suggestion that scrapie and its analogues are caused by proteinaceous infectious agents (prions) which replicate by invading the translation process and altering ribosomal specificity is examined. It is found that anomalous aetiological features of scrapie infection are explained by the model. An analysis suggesting that the possibility of prion replication undermines the basis of current molecular biological theory is provided and it is concluded that the exclusive identification of biological information with nucleic acid sequences is unjustified.

Changes in activity and amount of active elongation factor 1 alpha in aging and immortal human fibroblast cultures

Stoichiometrically estimated amounts of active elongation factor, EF-1 alpha, remain constant in serially passaged Phase II cultures of human fibroblasts, MRC-5, but decrease by 45% towards the end (Phase III) of their lifespan. Catalytic activity of EF-1 alpha is also reduced by 35% in Phase III old cells. The SV40 transformed immortal cell line MRC-5V2 has 30% higher levels of active EF-1 alpha without significant increase in its catalytic activity. Low-serum-associated G1 arrest of normal and transformed cells reduces amounts of active EF-1 alpha by 35% and 20%, respectively. Catalytic activity, however, is reduced rapidly only in G1 arrested normal cells and not in transformed cells. Even though the cell cycle-related changes are reversible both in normal and transformed cells, the age-related decline in amounts of active EF-1 alpha and its activity are irreversible and, most probably, crucial.