Ribosomal Protein Fraction Research Articles

Exponential trajectories, cell size fluctuations, and the adder property in bacteria follow from simple chemical dynamics and division control.

Experiments on steady-state bacterial cultures have uncovered several quantitative regularities at the system level. These include, first, the exponential growth of cell size with time and the balanced growth of intracellular chemicals between cell birth and division, which are puzzling given the nonlinear and decentralized chemical dynamics in the cell. We model a cell as a set of chemical populations undergoing nonlinear mass action kinetics in a container whose volume is a linear function of the chemical populations. This turns out to be a special class of dynamical systems that generically has attractors in which all populations grow exponentially with time at the same rate. This explains exponential balanced growth of bacterial cells without invoking any regulatory mechanisms and suggests that this could be a robust property of protocells as well. Second, we consider the hypothesis that cells commit themselves to division when a certain internal chemical population reaches a threshold of N molecules. We show that this hypothesis leads to a simple explanation of some of the variability observed across cells in a bacterial culture. In particular, it reproduces the adder property of cell size fluctuations observed recently in E. coli; the observed correlations among interdivision time, birth volume, and added volume in a generation; and the observed scale of the fluctuations (CV ≈ 10-30%) when N is between 10 and 100. Third, upon including a suitable regulatory mechanism that optimizes the growth rate of the cell, the model reproduces the observed bacterial growth laws including the dependence of the growth rate and ribosomal protein fraction on the medium. Thus, the models provide a framework for unifying diverse aspects of bacterial growth physiology under one roof. They also suggest new questions for experimental and theoretical enquiry.

Genome Wide Phosphoproteome Analysis of Zymomonas mobilis Under Anaerobic, Aerobic, and N2-Fixing Conditions.

Protein phosphorylation is a post-translational modification with widespread regulatory roles in both eukaryotes and prokaryotes. Using mass spectrometry, we performed a genome wide investigation of protein phosphorylation in the non-model organism and biofuel producer Zymomonas mobilis under anaerobic, aerobic, and N2-fixing conditions. Our phosphoproteome analysis revealed 125 unique phosphorylated proteins, belonging to major pathways such as glycolysis, TCA cycle, electron transport, nitrogen metabolism, and protein synthesis. Quantitative analysis revealed significant and widespread changes in protein phosphorylation across growth conditions. For example, we observed increased phosphorylation of nearly all glycolytic enzymes and a large fraction of ribosomal proteins during aerobic and N2-fixing conditions. We also observed substantial changes in the phosphorylation status of enzymes and regulatory proteins involved in nitrogen fixation and ammonia assimilation during N2-fixing conditions, including nitrogenase, the Rnf electron transport complex, the transcription factor NifA, GS-GOGAT cycle enzymes, and the PII regulatory protein. This suggested that protein phosphorylation may play an important role at regulating all aspects of nitrogen metabolism in Z. mobilis. This study provides new knowledge regarding the specific pathways and cellular processes that may be regulated by protein phosphorylation in this important industrial organism and provides a useful road map for future experiments that investigate the physiological role of specific phosphorylation events in Z. mobilis.

Verification of Ribosomal Proteins of Aspergillus fumigatus for Use as Biomarkers in MALDI-TOF MS Identification.

We have previously proposed a rapid identification method for bacterial strains based on the profiles of their ribosomal subunit proteins (RSPs), observed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). This method can perform phylogenetic characterization based on the mass of housekeeping RSP biomarkers, ideally calculated from amino acid sequence information registered in public protein databases. With the aim of extending its field of application to medical mycology, this study investigates the actual state of information of RSPs of eukaryotic fungi registered in public protein databases through the characterization of ribosomal protein fractions extracted from genome-sequenced Aspergillus fumigatus strains Af293 and A1163 as a model. In this process, we have found that the public protein databases harbor problems. The RSP names are in confusion, so we have provisionally unified them using the yeast naming system. The most serious problem is that many incorrect sequences are registered in the public protein databases. Surprisingly, more than half of the sequences are incorrect, due chiefly to mis-annotation of exon/intron structures. These errors could be corrected by a combination of in silico inspection by sequence homology analysis and MALDI-TOF MS measurements. We were also able to confirm conserved post-translational modifications in eleven RSPs. After these verifications, the masses of 31 expressed RSPs under 20,000 Da could be accurately confirmed. These RSPs have a potential to be useful biomarkers for identifying clinical isolates of A. fumigatus.

Direct Bacterial Profiling by Matrix-Assisted Laser Desorption−Ionization Time-of-Flight Mass Spectrometry for Identification of Pathogenic Neisseria

The present study investigates the suitability of direct bacterial profiling as a tool for the identification and subtyping of pathogenic Neisseria. The genus Neisseria includes two human pathogens, Neisseria meningitidis and Neisseria gonorrhoeae, as well as several nonpathogenic Neisseria species. Here, a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling protocol was optimized using a laboratory strain of E. coli DH5alpha to guarantee high quality and reproducible results. Subsequently, mass spectra for both laboratory and clinical strains of N. gonorrhoeae, N. meningitidis, and several nonpathogenic Neisseria species were collected. Significant interspecies differences but little intraspecies diversity were revealed by means of a visual inspection and bioinformatics examination using the MALDI BioTyper software. Cluster analysis successfully separated mass spectra collected from three groups that corresponded to N. gonorrhoeae, N. meningitidis, and nonpathogenic Neisseria isolates. Requiring only one bacterial colony for testing and using a fast and easy measuring protocol, this approach represents a powerful tool for the rapid identification of pathogenic Neisseria and can be adopted for other microorganisms.

Developing Limited Proteolysis and Mass Spectrometry for the Characterization of Ribosome Topography

An approach that combines limited proteolysis and matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has been developed to probe protease-accessible sites of ribosomal proteins from intact ribosomes. Escherichia coli and Thermus thermophilus 70S ribosomes were subjected to limited proteolysis using different proteases under strictly controlled conditions. Intact ribosomal proteins and large proteolytic peptides were recovered and directly analyzed by MALDI-MS, which allows for the determination of proteins that are resistant to proteolytic digestion by accurate measurement of molecular weights. Larger proteolytic peptides can be directly identified by the combination of measured mass, enzyme specificity, and protein database searching. Sucrose density gradient centrifugation revealed that the majority of the 70S ribosome dissociates into intact 30S and 50S subunits after 120 min of limited proteolysis. Thus, examination of ribosome populations within the first 30 to 60 min of incubation provides insight into 70S structural features. Results from E. coli and T. thermophilus revealed that a significantly larger fraction of 50S ribosomal proteins have similar limited proteolysis behavior than the 30S ribosomal proteins of these two organisms. The data obtained by this approach correlate with information available from the high-resolution crystal structures of both organisms. This new approach will be applicable to investigations of other large ribonucleoprotein complexes, is readily extendable to ribosomes from other organisms, and can facilitate additional structural studies on ribosome assembly intermediates.

5-Fluorouracil Activation of p53 Involves an MDM2-Ribosomal Protein Interaction

5-fluorouracil (5-FU) is a widely used chemotherapeutic drug for the treatment of a variety of solid tumors. The anti-tumor activity of 5-FU has been attributed in part to its ability to induce p53-dependent cell growth arrest and apoptosis. However, the molecular mechanisms underlying p53 activation by 5-FU remain largely obscure. Here we report that 5-FU treatment leads to p53 stabilization and activation by blocking MDM2 feedback inhibition through ribosomal proteins. 5-FU treatment increased the fraction of ribosome-free L5, L11, and L23 ribosomal proteins and their interaction with MDM2, leading to p53 activation and G1/S arrest. Conversely, individual knockdown of these ribosomal proteins by small interfering RNA prevented the 5-FU-induced p53 activation and reversed the 5-FU-induced G1/S arrest. These results demonstrate that 5-FU treatment triggers a ribosomal stress response so that ribosomal proteins L5, L11, and L23 are released from ribosome to activate p53 by ablating the MDM2-p53 feedback circuit.

Stimulation of the synthesis of ribosomal proteins in regenerating rat liver with special reference to the increase in the amounts of effective mRNAs for ribosomal proteins.

1 Normal and partially hepatectomized rats were pulse labeled for 15 min with [14C]leucine and [3H]leucine respectively. Both kinds of liver homogenates were mixed and the ribosomal protein fraction was purified from the mixed homogenate by chromatographic procedures. The 3H/14C ratio of this fraction was about three times higher than that of total protein, indicating that the synthesis of ribosomal proteins is selectively increased in regenerating rat liver. 2 The free polysomes from normal or regenerating rat livers were incubated with [3H]leucine in the presence of regenerating rat liver supernatant. Ribosomal proteins were then purified, finally by two-dimensional acrylamide gel electrophoresis. Biosyntheses of most of ribosomal proteins by regenerating rat liver polysomes were about 2.5 to 3.6 times higher than those by normal rat liver polysomes. 3 Using a wheat germ cell-free system, the template activities of poly(A)-containing mRNAs for ribosomal proteins were compared between normal and regenerating rat livers. The template activities at 6, 12, 18, 24 and 48 h after partial hepatectomy were about 1.3, 1.8, 2.4, 1.5 and 1.3 times higher, respectively, than the activity of normal rat liver. The extents of increase in the template activity of poly(A)-containing mRNAs for most of individual ribosomal proteins separated by two-dimensional gel electrophoresis were not so different at 18 h after the operation and the average template activity was 2.8 times higher than that of normal rat liver. The enhanced activity of regenerating rat liver for ribosomal protein synthesis is mainly caused by the increase in the apparent concentrations of mRNAs for ribosomal proteins.

Characterization of acidic ribosomal proteins from three developmental stages of the medfly Ceratitis capitata.

Acidic proteins extracted with 0.5 M NH4Cl and 50% ethanol from ribosomes of the medfly Ceratitis capitata showed two major bands of MW 15 and 17 kD after SDS electrophoresis. Isoelectrofocusing of acidic proteins resolved two groups of bands at pH 4.5 and 3.5. Similar patterns were observed both from the acidic ribosomal protein fraction and from total ribosomes, treated with RNase. Treatment with alkaline phosphatase reduced the number of bands with a shift to a higher pI, indicating dephosphorylation. The phosphorylation pattern of the acidic proteins changed at three different stages of development, six day larvae, white pupae and 0-2 days old embryos. The two protein groups correspond to multi-phosphorylated forms of eucaryotic acidic ribosomal proteins P1 and P2. This was shown by immunoblotting with specific monoclonal antibodies.

Large-scale preparation of fully deuterated cell components. Ribosomes from Escherichia coli with high biological activity.

Some applications of NMR and of neutron scattering require fully deuterated biological material which should be highly active and available in large quantities. These requirements are hardly compatible since full deuteration is achieved easily only if cells are grown in minimal media. This condition used in standard batch fermentation results in both low yields and reduced activities of the biological mass. Here we report a method which combines the apparently incompatible requirements taking advantage of a recent observation according to which the appearance of growth inhibiting extracellular products could be prevented. The method was applied for growing Escherichia coli cells, strain MRE600rif (resistance against high doses of rifampicin is used as selection marker) on partially deuterated media (76% and 84% D2O) with glucose as carbon source and on deuterated acetate and succinate with 100% D2O when full deuteration was to be achieved. The essential point for preserving the log-phase character of the cells is that the cultivation is carried out at substrate limiting conditions thus keeping the growth rate at low levels (for glucose the growth rate, mu < or = 0.35 h-1, for acetate/succinate mu < or = 0.1 h-1) which avoids the accumulation of the substrate or of by-products in the medium. Our data suggest that acetate is a main extracellular component for accompanying or triggering the transition from logarithmic growth to stationary phase of E. coli cells cultivated on glucose as carbon source. The cells were first grown in fed-batch to high cell densities (above 50 g wet cells/l) under conditions of substrate limitations. A steady-flow fermentation followed keeping the growth rate at about mu of 0.1 h-1. Cells were harvested in kg quantities, the extracted ribosomes showed a normal complement of proteins, contained intact rRNA and were fully active. The ribosomal protein and rRNA fractions could be efficiently reconstituted to highly active particles. In the case of full deuteration a matching point of 120% (tentative D2O scale) was achieved. The reported method facilitates the preparation of deuterated biological material for applications in NMR and neutron scattering analysis.

Identification and characterization of aDictyostelium discoideumribosomal protein gene

We have identified a developmentally repressed large-subunit ribosomal protein gene of Dictyostelium discoideum based on sequence similarity to other ribosomal proteins. Protein rpl7 is homologous to large subunit ribosomal proteins from the rat and possibly to Mycoplasma capricolum and Escherichia coli, but is not similar to three sequenced ribosomal proteins in Dictyostelium. The rpl7 gene is present at one copy per genome, as are six other cloned Dictyostelium ribosomal proteins. Restriction fragment length polymorphisms exist for ribosomal protein genes rpl7, rp1024, and rp110 in strain HU182; most Dictyostelium ribosomal protein genes examined are linked no closer than 30-100 kb to each other in the genome. Dictyostelium ribosomal proteins are known to be developmentally regulated, and levels of rpl7 transcript gradually decrease during the 24-hour development cycle. This drop correlates with that of rp1024, indicating these and other ribosomal protein genes may be coordinately regulated. To determine the cellular location of the protein, we raised antibodies to an rpl7-derived branched synthetic peptide. These antibodies cross-reacted with one protein of the expected size in a ribosomal protein fraction of Dictyostelium, indicating that the product of gene rpl7 is localized in the ribosome.

Partial reconstitution of 60S ribosomal subunits from yeast

Ribosomal 60S subunits active in polyphenylalanine synthesis can be reconstituted from core particles lacking 20-40% of the total protein. These core particles were obtained by treatment of yeast 60S subunits with dimethylmaleic anhydride, a reagent for protein amino groups. Upon reconstitution a complementary amount of split proteins is incorporated into the ribosomal particles, which have the sedimentation coefficient of the original subunits. Ribosomal protein fractions obtained by extraction with 1.25 M NH4Cl, 4 M LiCl, 7 M LiCl, or 67% acetic acid, are much less efficient in the reconstitution of active subunits from these core particles than the corresponding released fraction prepared with dimethylmaleic anhydride. Attempts to reconstitute active subunits from protein-deficient particles obtained with 1.25 M NH4Cl plus different preparations of ribosomal proteins, including the fraction released with dimethylmaleic anhydride, were unsuccessful. Therefore, under our conditions, of the disassembly procedures assayed only dimethylmaleic anhydride allows partial reconstitution of active 60S subunits.

Ribosomal subunit antiassociation activity in rabbit reticulocyte lysates. Evidence for a low molecular weight ribosomal subunit antiassociation protein factor (Mr = 25,000).

A ribosomal subunit antiassociation activity has been purified from both the postribosomal supernatant and ribosomal salt-wash protein fractions of rabbit reticulocyte lysates. A majority (greater than 90%) of the activity is associated with a low molecular weight protein of Mr of approximately 25,000. A small but significant level of antiassociation activity (less than 10%) was found to be associated with higher molecular weight protein fractions. The purified 25,000-dalton antiassociation factor interacts with 60 S ribosomal subunits to prevent them from reassociating with 40 S ribosomal subunits. The factor does not seem to interact directly with 40 S subunits nor does it dissociate 80 S monosomes. The properties of this factor are thus similar to the eukaryotic initiation factor 6 isolated from both wheat germ and calf liver extracts.

Effects of low dose actinomycin D treatment in vivo on the biosynthesis of ribosomal proteins in rat liver.

The long-term effects (up to 12 h) of low dose in vivo actinomycin D treatment, which selectively inhibits rRNA synthesis, on the activity of rat liver for the synthesis of ribosomal proteins relative to that for the synthesis of total protein were investigated. The effects of actinomycin D treatment in vivo and in vitro on the template activity of poly(A)-containing mRNA of rat liver for ribosomal proteins were examined by using a wheat germ cell-free system. The following results were obtained. 1. The activity of rat liver for synthesizing total protein observed in vivo and in vitro was inhibited by actinomycin D treatment even at a small dose. 2. A double-labeling technique using [3H] and [14C]leucine in vivo showed that the rate of synthesis of the ribosomal protein fraction relative to that of total protein in actinomycin-treated rat liver (6 + 6 h) was 1.45 times higher than that in the control rat. 3. By using a wheat germ cell-free system, it was shown that the template activity of poly(A)-containing mRNA for the synthesis of total protein was increased slightly by actinomycin D treatment in vivo. Furthermore, the template activity for the ribosomal protein fraction relative to that for total protein was increased. This increase was observed in most of the ribosomal proteins separated on two-dimensional acrylamide gel electrophoresis, although the extents of increase were different among individual ribosomal proteins examined. On the other hand, the selective increase of the template activity for the ribosomal protein fraction was not observed when poly(A)-containing mRNA was incubated with actinomycin D in vitro, although the template activity for total protein was increased slightly.

Humoral immunity to Streptococcus pneumoniae induced by a pneumococcal ribosomal protein fraction.

Isolation of a protective subfraction of ribosomes from Streptococcus pneumoniae has been achieved, and the immune response it induces has been investigated. Mice immunized with pneumococcal ribosomes or purified protein extracted from the ribosomal preparation (2-CE protein) exhibit similar survival rates upon challenge by virulent S. pneumoniae. In contrast, recipients of purified ribosomal ribonucleic acid were never protected against pneumococcal challenge. Serum from mice immunized with pneumococcal ribosomes or 2-CE protein passively immunized syngeneic recipients against pneumococcal challenge, whereas spleen cells from the same donors were unable to transfer immunity. Passive immunization with antiribosome serum could be abrogated by absorption with whole ribosomes, 2-CE protein, or various serotypes of S. pneumoniae (capsular types 2, 3, 6, and 14). Antiribosome serum significantly enhanced clearance of S. pneumoniae from mouse blood in vivo and in vitro. This required phagocytic cells, since antiribosome serum alone, with or without complement, supported growth of S. pneumoniae to an extent comparable to normal serum. The data suggest that the primary immunogen of pneumococcal ribosomes resides in the protein fraction. Further, the immunity induced by the protein fraction is mediated by antibody that appears to function as an opsonin for S. pneumoniae.

The conservation of amino acids in the n-terminal position of ribosomal and cytosol proteins from Escherichia coli, Bacillus stearothermophilus, and Halobacterium cutirubrum.

Alanine, methionine, and serine are the predominant N-terminal residues in the cytosol and ribosomal protein fractions from the thermophile Bacillus stear othermophilus and the extreme halophile Halobacterium cutirubrum, a similar situation to that previously found in Escherichia coli. In all three bacteria the N-terminal residues of the 30S ribosomal proteins are mainly alanine greater than methionine greater than serine whereas in the 50S ribosomal proteins from E. coli and B. stearothermophilus the predominant residues are methionine greater than alanine greater than serine suggesting conservation of specific N-terminal residues in these ribosomal proteins. However, the 50S ribosomal proteins from H. cutirubrum showed serine as the major N-terminal residue.

Role of precursor 16S RNA in assembly of E. coli 30S ribosomes.

RECONSTITUTION of bacterial ribosomes occurs in vitro in a system containing ribosomal components only1, which suggests that ribosomes also form by self-assembly in vivo. This inference is reinforced by the fact that intermediary particles, containing a similar fraction of ribosomal proteins, are observed both in vitro and in vivo1–3. The in vitro reconstitution process, however, requires a very high energy of activation, presumably to force the intermediates into a rare conformational state1,4. This requirement is too high to be compatible with the rate of ribosome formation in vivo5. Furthermore, there is evidence that the rate-limiting step which leads to the accumulation of the precursor particles in vivo does not involve spontaneous conformational change of these particles6. Although all the information, therefore, required to construct a ribosome must be present in its components, it seems that cells use an additional mechanism to facilitate their assembly.

The effect of β-ecdysone on protein synthesis in imaginal discs of Drosophila melanogaster cultured in vitro: II. Effects on synthesis in specific cell fractions

The effect of β-ecdysone on the synthesis of different proteins in imaginal discs of Drosophila melanogaster was investigated using double-label experiments and SDS acrylamide gel electrophoresis. Four different cellular fractions were analyzed (12K pellet, cytosol, core ribosomes, and KCl-soluble ribosomal proteins). β-Ecdysone alters the net synthesis of proteins in all of these fractions, with the most dramatic effects occurring in the ribosomal protein fractions. The maintenance of the altered pattern of synthesis of proteins in these fractions depends on the continued presence of β-ecdysone in the culture medium. The data suggest that β-ecdysone alters the synthesis of different proteins by acting on the genome. The apparent mechanisms by which β-ecdysone increases total protein synthesis and alters the net synthesis of different proteins in discs are discussed.

Acetylation of reticulocyte ribosomal proteins at time of protein biosynthesis.

When rabbit reticulocytes were incubated in vitro with [(3)H]acetate, their ribosomal proteins were rapidly acetylated within 10 min. Polyacrylamide-urea gel electrophoresis showed that several major ribosomal protein fractions were highly acetylated. By the double-isotope labeling technique, the incorporation of [(3)H]acetate and [(14)C]aminoacid mixture into ribosomal proteins and nascent chains was found to be closely associated. Sodium fluoride abolished the acetylation of ribosomal proteins, whereas cycloheximide reduced the acetylation of ribosomal proteins to a much lower level. These findings suggest that acetylation of ribosomal proteins may be involved in the formation of the initiation complex during protein biosynthesis.

Questioning the in vitro protein exchange between ribosomes and post-microsomal supernatant

We passed pure ribosomes from rat and kidney-bean through a radioactive rat liver post-microsomal supernatant. Although the total ribosomal protein fraction from both species became apparently labelled, fractionation of the proteins under suitable conditions indicated that they were not labelled. We thus question the possibility of extensive protein exchange between ribosomes and post-ribosomal supernatant.

A protein fraction of the 60 S subunit from reticulocyte ribosomes associated with acceptor-site binding activity

An electrophoretically distinct ribosomal protein fraction derived from the large (60 S) subunit of rabbit reticulocyte ribosomes appears to contain the sulfhydryl group(s), the integrity of which is required for the poly (U)-directed binding of phenylalanyl-transfer RNA. Since the addition of the translocase enzyme (T-2) is required to confer puromycin reactivity on these molecules, it is therefore assumed that they are in the acceptor site. This contrasts with studies in prokaryotic systems, which indicate that both N-ethyl maleimide sensitivity and the acceptor site are associated with the small ribosomal subunit. It is similar to that system, however, in that the proteins implicated have multiple sulfhydryl groups, and probably only one of these is required for phenylalanyl-transfer RNA binding activity.