Levels and rates of synthesis of ribosomal ribonucleic acid, transfer ribonucleic acid, and protein in Neurospora crassa in different steady states of growth

Shaping bacterial gene expression by physiological and proteome allocation constraints

Networks of molecular regulators are often the primary objects of focus in the study of gene regulation, with the machinery of protein synthesis tacitly relegated to the background. Shifting focus to the constraints imposed by the allocation of protein synthesis flux reveals surprising ways in which the actions of molecular regulators are shaped by physiological demands. Using carbon catabolite repression as a case study, we describe how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.

Evolutionary scaling of maximum growth rate with organism size

Data from nearly 1000 species reveal the upper bound to rates of biomass production achievable by natural selection across the Tree of Life. For heterotrophs, maximum growth rates scale positively with organism size in bacteria but negatively in eukaryotes, whereas for phototrophs, the scaling is negligible for cyanobacteria and weakly negative for eukaryotes. These results have significant implications for understanding the bioenergetic consequences of the transition from prokaryotes to eukaryotes, and of the expansion of some groups of the latter into multicellularity. The magnitudes of the scaling coefficients for eukaryotes are significantly lower than expected under any proposed physical-constraint model. Supported by genomic, bioenergetic, and population-genetic data and theory, an alternative hypothesis for the observed negative scaling in eukaryotes postulates that growth-diminishing mutations with small effects passively accumulate with increasing organism size as a consequence of associated increases in the power of random genetic drift. In contrast, conditional on the structural and functional features of ribosomes, natural selection has been able to promote bacteria with the fastest possible growth rates, implying minimal conflicts with both bioenergetic constraints and random genetic drift. If this extension of the drift-barrier hypothesis is correct, the interpretations of comparative studies of biological traits that have traditionally ignored differences in population-genetic environments will require revisiting.

Protein degradation sets the fraction of active ribosomes at vanishing growth

Growing cells adopt common basic strategies to achieve optimal resource allocation under limited resource availability. Our current understanding of such “growth laws” neglects degradation, assuming that it occurs slowly compared to the cell cycle duration. Here we argue that this assumption cannot hold at slow growth, leading to important consequences. We propose a simple framework showing that at slow growth protein degradation is balanced by a fraction of “maintenance” ribosomes. Consequently, active ribosomes do not drop to zero at vanishing growth, but as growth rate diminishes, an increasing fraction of active ribosomes performs maintenance. Through a detailed analysis of compiled data, we show that the predictions of this model agree with data from E. coli and S. cerevisiae. Intriguingly, we also find that protein degradation increases at slow growth, which we interpret as a consequence of active waste management and/or recycling. Our results highlight protein turnover as an underrated factor for our understanding of growth laws across kingdoms.

The idea that simple quantitative relationships relate cell physiology to cellular composition dates back to the 1950s, but the recent years saw a leap in our understanding of such “growth laws”, with relevant implications regarding the interdependence between growth, metabolism and biochemical networks. However, recent works on nutrient-limited growth mainly focused on laboratory conditions that are favourable to growth. Thus, our current mathematical understanding of the growth laws neglects protein degradation, under the argument that it occurs slowly compared to the timescale of the cell cycle. Instead, at slow growth the timescales of mass loss from protein degradation and dilution become comparable. In this work, we propose that protein degradation shapes the quantitative relationships between ribosome allocation and growth rate, and determines a fraction of ribosomes that do not contribute to growth and need to remain active to balance degradation.

An optimal growth law for RNA composition and its partial implementation through ribosomal and tRNA gene locations in bacterial genomes

The distribution of cellular resources across bacterial proteins has been quantified through phenomenological growth laws. Here, we describe a complementary bacterial growth law for RNA composition, emerging from optimal cellular resource allocation into ribosomes and ternary complexes. The predicted decline of the tRNA/rRNA ratio with growth rate agrees quantitatively with experimental data. Its regulation appears to be implemented in part through chromosomal localization, as rRNA genes are typically closer to the origin of replication than tRNA genes and thus have increasingly higher gene dosage at faster growth. At the highest growth rates in E. coli, the tRNA/rRNA gene dosage ratio based on chromosomal positions is almost identical to the observed and theoretically optimal tRNA/rRNA expression ratio, indicating that the chromosomal arrangement has evolved to favor maximal transcription of both types of genes at this condition.

Unlike the proteome composition, RNA composition is often assumed to be independent of growth rate in bacteria, despite experimental evidence for a growth rate dependence in many microbes. In this work, we derived a growth-rate dependent optimal tRNA/rRNA concentration ratio by minimizing the combined costs of ribosome and ternary complex at the required protein production rate. The predicted optimal tRNA/rRNA expression ratio, which is a monotonically decreasing function of growth rate, agrees with experimental data for E. coli and other fast-growing microbes. This indicates the existing of an RNA composition growth law. Due to the presence of partially replicated chromosomes, gene dosage is higher for those genes whose DNA is replicated earlier, an effect that becomes stronger at higher growth rates. Because rRNA genes are located closer to origin of replication than tRNA genes in fast-growing species, the tRNA/rRNA gene dosage ratio scales with growth rate in the same direction as the optimal tRNA/rRNA expression ratio. Thus, it appears that the RNA growth law is–at least in part–implemented simply through the genomic positions of tRNA and rRNA genes. This finding indicates that growth rate-dependent optimal resource allocation can influence the genomic organization in bacteria.

A large-scale nanoscopy and biochemistry analysis of postsynaptic dendritic spines

Dendritic spines, the postsynaptic compartments of excitatory neurotransmission, have different shapes classified from 'stubby' to 'mushroom-like'. Whereas mushroom spines are essential for adult brain function, stubby spines disappear during brain maturation. It is still unclear whether and how they differ in protein composition. To address this, we combined electron microscopy and quantitative biochemistry with super-resolution microscopy to annotate more than 47,000 spines for more than 100 synaptic targets. Surprisingly, mushroom and stubby spines have similar average protein copy numbers and topologies. However, an analysis of the correlation of each protein to the postsynaptic density mass, used as a marker of synaptic strength, showed substantially more significant results for the mushroom spines. Secretion and trafficking proteins correlated particularly poorly to the strength of stubby spines. This suggests that stubby spines are less likely to adequately respond to dynamic changes in synaptic transmission than mushroom spines, which possibly explains their loss during brain maturation.

Membranes, energetics, and evolution across the prokaryote-eukaryote divide

The evolution of the eukaryotic cell marked a profound moment in Earth’s history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes. Thus, although the origin of the mitochondrion was a key event in evolutionary history, there is no reason to think membrane bioenergetics played a direct, causal role in the transition from prokaryotes to eukaryotes and the subsequent explosive diversification of cellular and organismal complexity.

Over time, life on Earth has evolved into three large groups: archaea, bacteria, and eukaryotes. The most familiar forms of life – such as fungi, plants and animals – all belong to the eukaryotes. Bacteria and archaea are simpler, single-celled organisms and are collectively referred to as prokaryotes.

The hallmark feature that distinguishes eukaryotes from prokaryotes is that eukaryotic cells contain compartments called organelles that are surrounded by membranes. Each organelle supports different activities in the cell. Mitochondria, for example, are organelles that provide eukaryotes with most of their energy by producing energy-rich molecules called ATP. Prokaryotes lack mitochondria and instead produce their ATP on their cell surface membrane.

Some researchers have suggested that mitochondria might actually be one of the reasons that eukaryotic cells are typically larger than prokaryotes and more varied in their shape and structure. The thinking is that producing ATP on dedicated membranes inside the cell, rather than on the cell surface, boosted the amount of energy available to eukaryotic cells and allowed them to diversify more. However, other researchers are not convinced by this view. Moreover, some recent evidence suggested that eukaryotes are no more efficient in producing energy than prokaryotes.

Lynch and Marinov have now used computational and comparative analysis to compare the energy efficiency of different organisms including prokaryotes and eukaryotes grown under defined conditions. To do the comparison, the results were scaled based on cell volume and the total surface area deployed in energy production.

From their findings, Lynch and Marinov concluded that mitochondria did not enhance how much energy eukaryotes could produce per unit of cell volume in any substantial way. Although the origin of mitochondria was certainly a key event in evolutionary history, it is unlikely to have been responsible for the diversity and complexity of today’s life forms.

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

Maximization of growth rate is an important fitness strategy for bacteria. Bacteria can achieve this by expressing proteins at optimal concentrations, such that resources are not wasted. This is exemplified for Escherichia coli by the increase of its ribosomal protein-fraction with growth rate, which precisely matches the increased protein synthesis demand. These findings and others have led to the hypothesis that E. coli aims to maximize its growth rate in environments that support growth. However, what kind of regulatory strategy is required for a robust, optimal adjustment of the ribosome concentration to the prevailing condition is still an open question. In the present study, we analyze the ppGpp-controlled mechanism of ribosome expression used by E. coli and show that this mechanism maintains the ribosomes saturated with its substrates. In this manner, overexpression of the highly abundant ribosomal proteins is prevented, and limited resources can be redirected to the synthesis of other growth-promoting enzymes. It turns out that the kinetic conditions for robust, optimal protein-partitioning, which are required for growth rate maximization across conditions, can be achieved with basic biochemical interactions. We show that inactive ribosomes are the most suitable ‘signal’ for tracking the intracellular nutritional state and for adjusting gene expression accordingly, as small deviations from optimal ribosome concentration cause a huge fractional change in ribosome inactivity. We expect to find this control logic implemented across fast-growing microbial species because growth rate maximization is a common selective pressure, ribosomes are typically highly abundant and thus costly, and the required control can be implemented by a small, simple network.

Overexpression of Far1, a cyclin-dependent kinase inhibitor, induces a large transcriptional reprogramming in which RNA synthesis senses Far1 in a Sfp1-mediated way

The FAR1 gene encodes an 830 residue bifunctional protein, whose major function is inhibition of cyclin-dependent kinase complexes involved in the G1/S transition. FAR1 transcription is maximal between mitosis and early G1 phase. Enhanced FAR1 transcription is necessary but not sufficient for the pheromone-induced G1 arrest, since FAR1 overexpression itself does not trigger cell cycle arrest. Besides its well established role in the response to pheromone, recent evidences suggest that Far1 may also regulate the mitotic cell cycle progression: in particular, it has been proposed that Far1, together with the G1 cyclin Cln3, may be part of a cell sizer mechanism that controls the entry into S phase. Far1 is an unstable protein throughout the cell cycle except during G1 phase. Far1 levels peak in newborn cells as a consequence of a burst of synthetic activity at the end of the previous cycle, and the amounts per cell remain roughly constant during the G1 phase. Phosphorylation (at serine 87) by Cdk1-Cln complexes primes Far1 for ubiquitin-mediated proteolysis. By coupling a genome-wide transcriptional analysis of FAR1-overexpressing and far1Δ cells grown in ethanol- or glucose-supplemented minimal media with a range of phenotypic analysis, we show that FAR1 overexpression not only coordinately increases RNA and protein accumulation, but induces strong transcriptional remodeling, metabolism being the most affected cellular property, suggesting that the Far1/Cln3 sizer regulates cell growth either directly or indirectly by affecting metabolism and pathways known to modulate ribosome biogenesis. A crucial role in mediating the effect of Far1 overexpression is played by the Sfp1 protein, a key transcriptional regulator of ribosome biogenesis, whose presence is mandatory to allow a coordinated increase in both RNA and protein levels in ethanol-grown cells.

RNA:protein ratio of the unicellular organism as a characteristic of phosphorous and nitrogen stoichiometry and of the cellular requirement of ribosomes for protein synthesis

BACKGROUND

Mean phosphorous:nitrogen (P:N) ratios and relationships of P:N ratios with the growth rate of organisms indicate a surprising similarity among and within microbial species, plants, and insect herbivores. To reveal the cellular mechanisms underling this similarity, the macromolecular composition of seven microorganisms and the effect of specific growth rate (SGR) on RNA:protein ratio, the number of ribosomes, and peptide elongation rate (PER) were analyzed under different conditions of exponential growth.

RESULTS

It was found that P:N ratios calculated from RNA and protein contents in these particular organisms were in the same range as the mean ratios reported for diverse organisms and had similar positive relationships with growth rate, consistent with the growth-rate hypothesis. The efficiency of protein synthesis in microorganisms is estimated as the number of active ribosomes required for the incorporation of one amino acid into the synthesized protein. This parameter is calculated as the SGR:PER ratio. Experimental and theoretical evidence indicated that the requirement of ribosomes for protein synthesis is proportional to the RNA:protein ratio. The constant of proportionality had the same values for all organisms, and was derived mechanistically from the characteristics of the protein-synthesis machinery of the cell (the number of nucleotides per ribosome, the average masses of nucleotides and amino acids, the fraction of ribosomal RNA in the total RNA, and the fraction of active ribosomes). Impairment of the growth conditions decreased the RNA:protein ratio and increased the overall efficiency of protein synthesis in the microorganisms.

CONCLUSION

Our results suggest that the decrease in RNA:protein and estimated P:N ratios with decrease in the growth rate of the microorganism is a consequence of an increased overall efficiency of protein synthesis in the cell resulting from activation of the general stress response and increased transcription of cellular maintenance genes at the expense of growth related genes. The strong link between P:N stoichiometry, RNA:protein ratio, ribosomal requirement for protein synthesis, and growth rate of microorganisms indicated by the study could be used to characterize the N and P economy of complex ecosystems such as soils and the oceans.

Growth-rate-dependent adjustment of ribosome function in chemostat-grown cells of the fungus Mucor racemosus

The dimorphic fungus Mucor racemosus was grown as a yeast in a chemostat. Cellular growth rates were varied over a fourfold range under an atmosphere of N2 and over an eightfold range under CO2. Under either atmosphere, an increase in the cellular growth rate resulted in increases in (i) the cellular ribosome concentration, (ii) the percentage of ribosomes active in protein synthesis, and (iii) the rate of polypeptide chain elongation. The rate of protein synthesis in this organism can therefore be regulated by adjustment of all of these mechanisms.

Reduction of ribosome activity and synthesis of stable RNA in Neurospora crassa

The addition of cycloheximide (0.02 micrograms/ml) to exponentially growing cultures of Neurospora crassa causes a reduction in growth rate and a decrease in the rate of protein accumulation, due to a partial inhibition of protein synthesis, while RNA accumulation is unaffected for about 1 h. Thus, an increased RNA:protein ratio is established in the presence of the inhibitor. RNA that accumulates during treatment with cycloheximide has the same characteristics as that of the control cultures and this, together with the enhancement of the relative rate of synthesis of ribosomal proteins induced by cycloheximide, seems to indicate that more mature ribosomes are present in cycloheximide-treated cultures. The endocellular level of several amino acids begins to increase significantly only 60 min after cycloheximide addition. A possible explanation of the stimulation of ribosome production induced by cycloheximide is given in terms of the existence of a feed-back mechanism controlling ribosome synthesis.

Nuclear division cycle in Neurospora crassa hyphae under different growth conditions

Treatment with picolinic acid blocked Neurospora crassa nuclei in G1, and recovery from the treatment allowed a synchronous wave of deoxyribonucleic acid synthesis to occur. Nuclei, which appeared as compact globular bodies during the period of blockage, assumed a ring shape during the following S phase, which was also maintained in the G2 phase. The proportion of compact globular nuclei was much higher in hyphae growing at lower rates, whereas that of ring nuclei increased when the hyphae were growing at higher rates. Horseshoe nuclei (probably mitotic nuclei) and double ring nuclei were also observed in growing hyphae, but their frequencies were low and fairly independent of the rate of growth. The length of the S phase of the Neurospora nuclear division cycle was determined to be about 30 min. From the frequencies of the phase-specific nuclear shapes, the durations of the G1 phase and the combined S plus G2 phases were calculated. The results showed that variations in the growth rates of the mycelia were mainly coupled with variations in the G1 phase of the nuclear division cycle. For mycelia growing in minimal sucrose, the lengths of all of the phases of the nuclear division cycle were estimated.

Physiological control of phosphorylation ribosomal protein S6 in Mucor racemosus

The level of phosphorylation of ribosomal protein S6 increased with accelerating rates of growth and protein synthesis in Mucor racemosus. Lowered levels of phosphorylation were seen under conditions of metabolic shift-down or the onset of stationary phase, and no phosphorylation was detected in sporangiospores. Changing metabolic states, changing intracellular levels of adenosine triphosphatase, and the level of phosphorylation of protein S6 were correlated in M. racemosus.

Level and turnover of polyadenylate-containing ribonucleic acid in Neurospora crassa in different steady states of growth

Mycelia of Neurospora crassa in a steady state of growth in different media have a ribosomal content proportional to the rate of growth. Moreover, both the percentage of polysomes and the average ribosomal activity are about the same at all different growth rates. The content of polyadenylated RNA was determined in three different conditions of exponential growth, which allowed growth rates that ranged from 0.26 to 0.51 duplications/h, and was found to constitute about the same fraction of total RNA (4.5--5.2%). Using a kinetic approach, an equation was derived which allowed determination of the average half-lives of polyadenylated RNA: in each medium the cultures were labeled from the moment of the inoculation with [32P]orthophosphate and were then given a 10-min pulse with [5-3H]uridine when they were in the exponential phase. It was found that the determined half-lives of polyadenylated RNA vary, depending on the growth medium, between 30 and 60 min, but with no direct correlation with the growth rate. Moreover, the rate of synthesis of polyadenylated RNA relative to that of stable RNA decreased with the growth rate. On the basis of previous data on the rates of synthesis of stable RNA, it was possible to make an evaluation of the absolute rate of synthesis of polyadenylated RNA. Whereas the rate of synthesis of stable ribosomal RNA increases as a function of the square of the number of duplications per hour, the increase in the rate of synthesis of polyadenylated RNA with the growth rate is much less consistent. It is concluded that in Neurospora the growth rate does not depend on the rate of synthesis of mRNA but rather on the rate of synthesis of rRNA, which sets both the ribosomal level and the steady-state level of mRNA.

Regulation of macromolecular synthesis during hyphal germ tube emergence from Mucor racemosus sporangiospores

Protein and RNA syntheses were examined during hyphal germ tube emergence from sporangiospores of a dimorphic phycomycete, Mucor racemosus. Both classes of macromolecules were synthesized immediately upon introduction of the dormant sporangiospores into nutrient medium. The specific rates of synthesis of both protein and RNA accelerated during initial germ tube emergence and reached a maximum when the emergence of new germ tubes ended. The specific rates of synthesis later decreased during further hyphal elongation. The distribution of ribosomes between active polysomes and monosomes and inactive subunits was determined by sucrose density gradient centrifugation, and the rate of amino acid addition to nascent polypeptide chains was calculated throughout the developmental sequence. The results showed that both the percentage of ribosomes active in protein synthesis and the velocity of ribosome movement along the mRNA were continuously adjusted throughout hyphal germ tube development. The free intracellular amino acid pools were measured throughout development. Alanine, glutamate, and aspartate were present at very high concentrations in the dormant spores but were rapidly depleted during hyphal germ tube emergence. The results of these studies are discussed in relation to hyphal germ tube development from yeast cells of Mucor and dormant spores of other fungal species.

Levels of the ribonucleoside triphosphates and rate of RNA synthesis in Neurospora crassa

The levels of the four ribonucleoside triphosphate (ATP, GTP, UTP and CTP) have been determined in Neurospora crassa in three conditions of exponential growth (on glucose, acetate and glycerol) as well as in the course of a shift-up and a shift-down transition of growth between two of them. Although in some cases the pools appear proportional to the rate of synthesis of ribosomal RNA, this seems not to be strictly dependent on the level of the nucleotides.

Dynamics of cellular growth

The assumption that prompted the studies reported in this paper was that the unsatisfactory state of our knowledge on the regulation of cellular growth might derive from the reductionistic approach used to investigate it. Thus an analysis of cellular growth which applied concepts derived from systems dynamics was undertaken. First of all a dynamic model of cellular growth has been constructed. It has the following features: the levels of DNA, ribosomes and proteins are the defining levels; cellular growth is expressed by a close loop in which the level of ribosomes per genome and, indirectly, the level of proteins per genome are stabilized around goal values by the action of negative feed backs. The validity of the model has been tested by its ability to predict the growth kinetics of a real system (exponentially growing Neurospora cells). The simulated growth has been found to reproduce with great accuracy that of Neurospora cells. A slightly modified model, which takes into consideration also the degradation of ribosomes and of proteins, is shown to predict with accuracy the dynamics of growth of both growing and resting fibroblasts. These latter results suggest that the rates of macromolecular turnovers play a central role in the control of proliferation of mammalian cells: the condition of zero growth seems to be achieved when the rate of synthesis and the rate of degradation of proteins are the same. The possibility is discussed that the model indicates a unifying hypothesis of the mode of action of growth controlling conditions (hormones, growth factors, contact inhibition).