Heterogeneity of ribosomal populations in Escherichia coli cells grown in different media

Reconsidering Dogmas about the Growth of Bacterial Populations

The growth of bacterial populations has been described as a dynamic process of continuous reproduction and cell death. However, this is far from the reality. In a well fed, growing bacterial population, the stationary phase inevitably occurs, and it is not due to accumulated toxins or cell death. A population spends the most time in the stationary phase, where the phenotype of the cells alters from the proliferating ones, and only the colony forming unit (CFU) decreases after a while, not the total cell concentration. A bacterial population can be considered as a virtual tissue as a result of a specific differentiation process, in which the exponential-phase cells develop to stationary-phase cells and eventually reach the unculturable form. The richness of the nutrient had no effect on growth rate or on stationary cell density. The generation time seems not to be a constant value, but it depended on the concentration of the starter cultures. Inoculations with serial dilutions of stationary populations reveal a so-called minimal stationary cell concentration (MSCC) point, up to which the cell concentrations remain constant upon dilutions; that seems to be universal among unicellular organisms.

Ribosome Specialization in Protozoa Parasites

Ribosomes, in general, are viewed as constitutive macromolecular machines where protein synthesis takes place; however, this view has been recently challenged, supporting the hypothesis of ribosome specialization and opening a completely new field of research. Recent studies have demonstrated that ribosomes are heterogenous in their nature and can provide another layer of gene expression control by regulating translation. Heterogeneities in ribosomal RNA and ribosomal proteins that compose them favor the selective translation of different sub-pools of mRNAs and functional specialization. In recent years, the heterogeneity and specialization of ribosomes have been widely reported in different eukaryotic study models; however, few reports on this topic have been made on protozoa and even less on protozoa parasites of medical importance. This review analyzes heterogeneities of ribosomes in protozoa parasites highlighting the specialization in their functions and their importance in parasitism, in the transition between stages in their life cycle, in the change of host and in response to environmental conditions.

The RNA ligase RtcB reverses MazF-induced ribosome heterogeneity in Escherichia coli

When Escherichia coli encounters stress, the endoribonuclease MazF initiates a post-transcriptional response that results in the reprogramming of protein synthesis. By removing the 3΄-terminus of the 16S rRNA, MazF generates specialized ribosomes that selectively translate mRNAs likewise processed by MazF. Given the energy required for de novo ribosome biosynthesis, we considered the existence of a repair mechanism operating upon stress relief to recycle the modified ribosomes. Here, we show that the stress-ribosomes and the 3΄-terminal 16S rRNA fragment are stable during adverse conditions. Moreover, employing in vitro and in vivo approaches we demonstrate that the RNA ligase RtcB catalyzes the re-ligation of the truncated 16S rRNA present in specialized ribosomes Thereby their ability to translate canonical mRNAs is fully restored. Together, our findings not only provide a physiological function for the RNA ligase RtcB in bacteria but highlight the reversibility of ribosome heterogeneity, a crucial but hitherto undescribed concept for translational regulation.

Alterations of the translation apparatus during aging and stress response

Aging is a biological process characterized by the irreversible and time-dependent deterioration of cell functions, tissues, and organs. Accumulating studies in a wide range of species from yeast to human revealed changes associated with the aging process to be conserved throughout evolution. The main characteristics of aging are (i) genomic instability, (ii) loss of telomere function, (iii) epigenetic changes,(iv) increased cellular senescence, (v) depletion of the stem cell pool, (vi) altered intercellular communication and (vii) loss of protein homeostasis. Among the multiple molecular mechanisms underlying aging, alterations of the translation machinery affecting the rate and selectivity of protein biosynthesis seem to play a central role. At the very heart of translation is the ribosome, a multifaceted and universally conserved RNA-protein particle responsible for accurate polypeptide synthesis and co-translational protein folding. Here we summarize and discuss recent developments on the contribution of altered translation and age-dependent modifications on the ribosome structure to aging and cellular senescence.

Translating the genome in time and space: specialized ribosomes, RNA regulons, and RNA-binding proteins

A central question in cell and developmental biology is how the information encoded in the genome is differentially interpreted to generate a diverse array of cell types. A growing body of research on posttranscriptional gene regulation is revealing that both global protein synthesis rates and the translation of specific mRNAs are highly specialized in different cell types. How this exquisite translational regulation is achieved is the focus of this review. Two levels of regulation are discussed: the translation machinery and cis-acting elements within mRNAs. Recent evidence shows that the ribosome itself directs how the genome is translated in time and space and reveals surprising functional specificity in individual components of the core translation machinery. We are also just beginning to appreciate the rich regulatory information embedded in the untranslated regions of mRNAs, which direct the selective translation of transcripts. These hidden RNA regulons may interface with a myriad of RNA-binding proteins and specialized translation machinery to provide an additional layer of regulation to how transcripts are spatiotemporally expressed. Understanding this largely unexplored world of translational codes hardwired in the core translation machinery is an exciting new research frontier fundamental to our understanding of gene regulation, organismal development, and evolution.

Heterogeneity of the translational machinery: Variations on a common theme

In all organisms the universal process of protein synthesis is performed by the ribosome, a complex multi-component assembly composed of RNA and protein elements. Although ribosome heterogeneity was observed already more than 40 years ago, the ribosome is still traditionally viewed as an unchangeable entity that has to be equipped with all ribosomal components and translation factors in order to precisely accomplish all steps in protein synthesis. In the recent years this concept was challenged by several studies highlighting a broad variation in the composition of the translational machinery in response to environmental signals, which leads to its adaptation and functional specialization. Here, we summarize recent reports on the variability of the protein synthesis apparatus in diverse organisms and discuss the multiple mechanisms and possibilities that can lead to functional ribosome heterogeneity. Collectively, these results indicate that all cells are equipped with a remarkable toolbox to fine tune gene expression at the level of translation and emphasize the physiological importance of ribosome heterogeneity for the immediate implementation of environmental information.

Mitoribosomal regulation of OXPHOS biogenesis in plants

The ribosome filter hypothesis posits that ribosomes are not simple non-selective translation machines but may also function as regulatory elements in protein synthesis. Recent data supporting ribosomal filtering come from plant mitochondria where it has been shown that translation of mitochondrial transcripts encoding components of oxidative phosphorylation complexes (OXPHOS) and of mitoribosomes can be differentially affected by alterations in mitoribosomes. The biogenesis of mitoribosome was perturbed by silencing of a gene encoding a small-subunit protein of the mitoribosome in Arabidopsis thaliana. As a consequence, the mitochondrial OXPHOS and ribosomal transcripts were both upregulated, but only the ribosomal proteins were oversynthesized, while the OXPHOS subunits were actually depleted. This finding implies that the heterogeneity of plant mitoribosomes found in vivo could contribute to the functional selectivity of translation under distinct conditions. Furthermore, global analysis indicates that biogenesis of OXPHOS complexes in plants can be regulated at different levels of mitochondrial and nuclear gene expression, however, the ultimate coordination of genome expression occurs at the complex assembly level.

Ribosome heterogeneity: another level of complexity in bacterial translation regulation

Translation of the mRNA-encoded genetic information into proteins is catalyzed by the intricate ribonucleoprotein machine, the ribosome. Historically, the bacterial ribosome is viewed as an unchangeable entity, constantly equipped with the entire complement of RNAs and proteins. Conversely, several lines of evidence indicate the presence of functional selective ribosomal subpopulations that exhibit variations in the RNA or the protein components and modulate the translational program in response to environmental changes. Here, we summarize these findings, which raise the functional status of the ribosome from a protein synthesis machinery only to a regulatory hub that integrates environmental cues in the process of protein synthesis, thereby adding an additional level of complexity to the regulation of gene expression.

A top-down/bottom-up study of the ribosomal proteins of Caulobacter crescentus

Ribosomes from the Gram-negative alpha-proteobacterium Caulobacter crescentus were isolated using standard methods. Proteins were separated using a two-dimensional liquid chromatographic system that allowed the analysis of whole proteins by direct coupling to an ESI-QTOF mass spectrometer and of proteolytic digests by a number of mass spectrometric methods. The masses of 53 of 54 ribosomal proteins were directly measured. Protein identifications and proposed post-translational modifications were supported by proteolysis with trypsin, endoprotease Glu-C, and exoproteases carboxypeptidases Y and P. Tryptic peptide mass maps show an average sequence coverage of 62%, and carboxypeptidase C-terminal sequence tagging provided unambiguous identification of the small, highly basic proteins of the large subunit. C. crescentus presents some post-translational modifications that are similar to those of Escherichia coli (e.g., N-terminal acetylation of S9 and S18) along with some unique variations, such as a near absence of L7 and extensive modification of L11. The comprehensive description of this organism's ribosomal proteome provides a foundation for the study of ribosome structure, dependence of post-translational modifications on growth conditions, and the evolution of subcellular organelles.

Structural investigations of the highly flexible recombinant ribosomal protein L12 from Thermotoga maritima

Ribosomal protein L7/L12, the only multicopy component of the ribosome, is involved in translation factor binding and in the ribosomal GTPase center. The gene for L7/L12 from Thermotoga maritima was cloned and the protein expressed at high levels in Escherichia coli. Purification of L7/L12 was achieved under non-denaturing conditions via heat treatment and two chromatographic steps. Circular dichroism melting profiles were monitored at 222 nm, showing the melting temperature of the protein at pH 7.5 around 110 degrees C, compared to approximately 60 degrees C for the highly homologous Escherichia coli protein. The unfolding was reversible and renaturation closely followed the path of the thermal melting. Dynamic light scattering, gel filtration chromatography, and crosslinking experiments suggested that under physiological buffer conditions Thermotoga maritima L7/L12 exists as a tetramer. The protein was crystallized under two conditions, yielding an orthorhombic (C222(1)) and a cubic (12(1)3) space group with an estimated two and three to four L7/L12 molecules per asymmetric unit, respectively. The crystals contained the full-length protein, and cryogenic buffers were developed which improved the mosaic spreads and the resolution limits. For the structure solution isoleucine was mutated to methionine at two separate positions, the mutant forms expressed as selenomethionine variants and crystallized.

Levels of major proteins of Escherichia coli during growth at different temperatures

The adaptation of Escherichia coli B/r to temperature was studied by measuring the levels of 133 proteins (comprising 70% of the cell's protein mass) during balanced growth in rich medium at seven temperatures from 13.5 to 46 degrees C. The growth rate of this strain in either rich or minimal medium varies as a simple function of temperature with an Arrhenius constant of approximately 13,500 cal (ca. 56,500 J) per mol from 23 to 37 degrees C, the so-called normal range; above and below this range the growth rate decreases sharply. Analysis of the detailed results indicates that (i) metabolic coordination within the normal (Arrhenius) range is largely achieved by modulation of enzyme activity rather than amount; (ii) the restricted growth that occurs outside this range is accompanied by marked changes in the levels of most of these proteins; (iii) a few proteins are thermometer-like in varying simply with temperature over the whole temperature range irrespective of the influence of temperature on cell growth; and (iv) the temperature response of half of the proteins can be predicted from current information on their metabolic role or from their variation in level in different media at 37 degrees C.

Post-translational modification of Escherichia coli ribosomal protein S6

Escherichia coli has multiple forms of ribosomal protein S6, differing in number of glutamyl resideus at the C-terminal end. Three forms are revealed when crude cell extracts are fractionated by a two-dimensional gel electrophoresis technique. Pulse-chase experiments show that the shortest and most alkaline form of S6 is the first to appear. In about one doubling time this form reaches equilibrium with the two other forms of S6, implicating the existence of an enzyme, which adds glutamic acid residues to S6. We show that the relative levels of these three S6 forms are not affected by the growth rate of the culture.

Quantitative variation of a 60S ribosomal protein during growth of the fungus Podospora anserina

During the growth phase, in the fungus Podospora anserina, a variation is observed in the composition of the ribosomal proteins. A protein of the 60S subunit which is absent in the ribosomes from 2 days old cultures becomes gradully more abundant as the culture time is prolonged.

Phenotypic instability in a tif-1 Mutant of Escherichia coli. I. Impairment in ribosomal function

The mutant T44(lambda) of Escherichia coli K12, grown in the presence of adenine, develops an increased tolerance to streptomycin. In cultures grown on streptomycin, the ts character (tif) may temporarily be suppressed but, on further transfer, both the temperature-sensitive phenotype and streptomycin tolerance disappear. In a cell-free system, the relative efficiency of translation of MS2 and poly U messenger RNAs was, respectively, 75 and 50% lower in extracts from cultures grown at 37 degrees with adenine than in extracts from 30 degrees cultures. Similar results were obtained when adenine was added in vitro to an extract from a culture grown at 37 degrees in the absence of adenine, using MS2 RNA as messenger. Moreover, the 37 degrees extracts showed a much lower misincorporation of isoleucine into polyphenylalanine in the poly U system. In addition, the Mg++ concentration required for optimal translational acitvity was higher for the 37 degrees than for the 30 degrees extracts. Extracts from a culture grown in L medium at 37 degrees or from a tif-/F'tif+ merodiploid grown at 37 degrees with adenine behaved similarly to that from the 30 degrees culture when poly U was used as messenger RNA. It is suggested that the tif+ gene product may play a regulatory role in ribosomal function and the pleiotropic nature of the tif-1 mutation could be due to impairment of translational activity augmented by elevated temperature or by adenine.

The stoichiometry of the ribosomal proteins of Escherichia coli

A ribosome preparation from E. coli made without stringent washing procedures has been shown to contain the same relative amounts of nearly all the ribosomal proteins as ribosomes in intact cells. Stoichiometric measurements on all the proteins of this preparation except for L8, L20, L31 and L34 have been made using an isotope dilution technique. When the scatter of the values obtained, the uncertainty in the molecular weights, and the losses occurring during extraction are taken into account, none of the proteins except L7/L12 is present at a level significantly different from one molecule per ribosome. There are multiple copies of L7/L12. These data suggest that the ribosomes of Escherichia coli are homogeneous in vivo.

Translational Control of Protein Synthesis in Staphylococcus aureus

The calculated in vivo polypeptide chain growth rate for Staphylococcus auteus MF-31 grown in nutritionally rich medium assuming all the ribosomes were functional was found to be approximately 16 amino acids/s/ribosome, but decreased to 10.2 amino acids/s/ribosome for cells grown in poor medium. An in vitro analysis revealed that 70S ribosomes isolated from rich medium cells were more active than similar 70S ribosomes derived from cells grown in poor medium. The 30S subunit was found responsible for the increased activity of the rich monosomes, whereas the 50S subunit appeared to be capable of either high or low activity.

Analysis of the ribosomes engaged in the synthesis of the outer membrane proteins of Escherichia coli

The messenger RNAs for the outer membrane proteins in E. coli are more stable than the bulk of the messenger RNA s (Hirashima et al., 1973). Polysomes, enriched in those containing stable mRNAs have been isolated following rifampicin treatment and have been shown to contain quantitatively the same complement of ribosomal protein as normal polysomes. There is one exception: ribosomal protein S1 is present in larger amounts in the polysomes containing stable messengers. However, there are grounds for believing this finding to be an artifact. It is concluded that the differences between outer membrane protein synthesis and bulk protein synthesis are not due to a difference in the ribosomes.

Variation of ribosomal proteins with bacterial growth rate

The composition of ribosomal proteins has been examined as a function of the growth rate of Escherichia coli cells. Seven sets of cultural conditions, utilizing different combinations of carbon and nitrogen sources, were employed to provide a 36-fold spread in growth rate. The cellular content of most of the ribosomal proteins in ribosomes decreased to a similar extent in the very slow-growing cultures. Major exceptions were proteins S6 and L12, which exhibited a much more pronounced decrease , and S21, which exhibited an increase. None of the proteins remained invariant with growth rate.

The protein topography of the E. coli 30S ribosomal subunit: a preliminary model E. coli/30S subunit/ribosome/spatial arrangement of proteins

A three dimensional model is presented which shows the apatial arrangement of 20 of the 21 proteins of the 30S ribosomal subunit of Escherichia coli. The model fulfills several purposes: (a) It summarizes currently available structural and functional data on ribosomal proteins; (b) It suggests an interesting correlation between stoichiometry and function. Functional proteins are both clustered and fractional; (c) It can be evaluated in relationships or point out critical experiments by which it can be tested.

Reductive alkylation of ribosomes as a probe to the topography of ribosomal proteins

Escherichia coli ribosomes were treated with a number of different aldehydes of various sizes in the presence of NaBH(4). After incorporation of either (3)H or (14)C, the ribosomal proteins were separated by two-dimensional polyacrylamide-gel electrophoresis and the extent of alkylation of the lysine residues in each protein was measured. The same pattern of alkylation was observed with the four reagents used, namely formaldehyde, acetone, benzaldehyde and 3,4,5-trimethoxybenzaldehyde. Every protein in 30S and 50S subunits was modified, although there was considerable variation in the degree of alkylation of individual proteins. A topographical classification of ribosomal proteins is presented, based on the degree of exposure of lysine residues. The data indicate that every protein of the ribosome has at least one lysine residue exposed at or near the surface of the ribonucleo-protein complex.

Alteration in the acetylation level of ribosomal protein L12 during growth cycle of Escherichia coli

The relative content in ribosomes of L7 and L12, the two forms of a protein in the 50S subunit specifically involved in GTP hydrolysis, is found to undergo a striking shift with the growth phase of E. coli. The content of L12 (nonacetylated form) increases during early logarithmic phase, becoming about 85% of the total before midlogarithmic phase. Thereafter, L7 (N-acetylated form) content begins to increase, eventually becoming 75-80% in stationary phase. The L7 + L12 content per ribosome, however, remained constant during this shift. Our evidence suggests that the shift did not occur through modification of preexisting ribosomes. The data further indicate that the E. coli cell may contain more than one structurally distinct (with regard to L7 or L12 content) 50S subunit population.

Function of individual 30S subunit proteins of Escherichia coli. Effect of specific immunoglobulin fragments (Fab) on activities of ribosomal decoding sites

Specific anti-30S protein immunoglobulin G fragments (Fab) were used to determine the contribution of each of the 30S ribosomal proteins to: (1) polyphenylalanine synthesis, (2) initiation factor-dependent binding of fMet-tRNA, (3) T-factor-dependent binding of phenylalanyl-tRNA, and (4) fixation of radioactive dihydrostreptomycin. Twenty of the 21 possible antibodies (antibody against S17 excepted) were used. In conditions where all the 30S proteins were accessible to Fabs, all of these monovalent antibodies strongly inhibited polyphenylalanine synthesis in vitro. Antibodies against S4, S6, S7, S12, S15, and S16, however, showed a weaker effect.30S proteins can be classified into four categories by their contributions to the function of sites "A" and "P": class I appears nonessential for tRNA positioning at either site (S4, S7, S15, and S16); class II includes proteins whose role in initiation is critical (S2, S5, S6, S12, and S13); class III (S8, S9, S11, and S18) corresponds to proteins whose blockade prevents internal (elongation factor Tudependent) positioning; and class IV includes entities that are essential for activities of both "A" and "P" sites (S1, S3, S10, S14, S19, S20, and S21). Dihydrostreptomycin fixation to the 30S or 70S ribosomes was inhibited by antibodies against S1, S10, S11, S18, S19, S20, and S21, but only weakly by the anti-S12 (Str A protein) Fab. The significance of these results is discussed in relation to 30S protein function, heterogeneity, and topography.