A platform for compartmentalized protein synthesis: protein translation and translocation in the ER

Recent advances in the study of protein translocation across the membrane of the endoplasmic reticulum include insights into the mechanism of signal-sequence function. Biochemical and genetic studies have provided further evidence that lumenal proteins perform direct roles in secretory protein translocation and in the regulation of protein-conducting-channel permeability during membrane protein integration. A hypothesis identifying the endoplasmic reticulum as a site of mRNA localization and compartmentalized protein synthesis has been suggested.     

Quantitative polysome analysis identifies limitations in bacterial cell-free protein synthesis

Cell-free protein synthesis (CFPS) is becoming increasingly used for protein production as yields increase and costs decrease. CFPS optimization efforts have focused primarily on energy supply and small molecule metabolism, though little is known about the protein synthesis machinery or what limits protein synthesis rates. Here, quantitative polysome profile analysis was used to characterize cell-free translation, thereby elucidating many kinetic parameters. The ribosome concentration in Escherichia coli-based CFPS reactions was 1.6 +/- 0.1 microM, with 72 +/- 4% actively translating at maximal protein synthesis rate. A translation elongation rate of 1.5 +/- 0.2 amino acids per second per ribosome and an initiation rate of 8.2 x 10(-9) +/- 0.3 x 10(-9) M/s, which correlates to, on average, one initiation every 60 +/- 9 s per mRNA, were determined. The measured CFPS initiation and elongation rates are an order of magnitude lower than the in vivo rates and further analysis identified elongation as the major limitation. Adding purified elongation factors (EFs) to CFPS reactions increased the ribosome elongation rate and protein synthesis rates and yields, as well as the translation initiation rate, indicating a possible coupling between initiation and elongation. Further examination of translation initiation in the cell-free system showed that the first initiation on an mRNA is slower than subsequent initiations. Our results demonstrate that polysome analysis is a valid tool to characterize cell-free translation and to identify limiting steps, that dilution of translation factors is a limitation of CFPS, and that CFPS is a useful platform for making novel observations about translation.     

Cholecystokinin-induced changes in polysome structure regulate protein synthesis in pancreas.

Translational regulation of digestive enzyme synthesis during short-term stimulation by cholecystokinin-octapeptide (CCK-OP), was examined in minced rabbit pancreas by measuring protein synthesis and monitoring alterations in the size of polysomes attached to the rough endoplasmic reticulum (RER). The effect of CCK-OP on protein synthesis was determined by measuring [3H]leucine incorporation into trichloroacetic-acid-precipitable proteins. Concentrations of CCK-OP that caused maximal enzyme secretion (10 and 30 nM) decreased protein synthesis by approx. 50% compared to control. Protein synthesis returned to the control level 60 min after terminating the action of CCK-OP. Autoradiography of [35S]methionine-labeled proteins separated by one-dimensional SDS-polyacrylamide gel electrophoresis demonstrated that CCK-OP reversibly inhibited the synthesis of all of the major groups of digestive enzymes. Northern blot analysis revealed that CCK-OP did not alter the cellular content of amylase and elastase mRNA. Incubation with CCK-OP caused a decrease in the size distribution of RER-bound polysomes. Polysome profiles returned to the control pattern 60 min following termination of the stimulus. These results suggest that the inhibitory effects of CCK-OP on the synthesis of digestive enzymes is regulated at translation by decreasing the number of RER-bound ribosomes that are actively translating digestive enzyme mRNA.     

A model of myoglobin self-organization

The self-organization of helical regions of myoglobin into a compact tertiary structure is considered on the basis of the hypothesis on the step-wise mechanism of self-organization of protein molecules. It is assumed that the self-organization begins with the formation of “ centers of crystallization ” and proceeds with the growth of one such center or by a sequential collapse of two or more grown centers.Different pathways of self-organization of myoglobin are considered; the most favourable structures corresponding to the greatest number of dehydrated bulky hydroptiobic groups and to all the strongly hydrophilic groups exposed to water are selected at every stage of the given pathway and the others are neglected. One of the two most favourable structures obtained in such a way coincides in rough resolution with the native tertiary structure of protein.     

A mathematical model for prokaryotic protein synthesis

A kinetic model for the synthesis of proteins in prokaryotes is presented and analysed. This model is based on a Markov model for the state of the DNA strand encoding the protein. The states that the DNA strand can occupy are: ready, repressed, or having a mRNA chain of length i in the process of being completed. The case i = 0 corresponds to the RNA polymerase attached, but no nucleotides attached to the chain. The Markov model consists of differential equations for the rates of change of the probabilities. The rate of production of the mRNA molecules is equal to the probability that the chain is assembled to the penultimate nucleotide, times the rate at which that nucleotide is attached. Similarly, the mRNA molecules can also be in different states, including: ready and having an amino acid chain of length j attached. The rate of protein synthesis is the rate at which the chain is completed. A Michaelis-Menten type of analysis is done, assuming that the rate of protein degradation determines the ’slow’ time, and that all the other kinetic rates are ‘fast’. In the self-regulated case, this results in a single ordinary differential equation for the protein concentration.     

Effects of phenobarbital on protein synthesis and polysome levels in rat liver.

Administration of phenobarbital to rats increases the rate of synthesis of certain microsomal drug-metabolizing enzymes in a selective manner and promotes proliferation of smooth endoplasmic reticulum in the liver. Phenobarbital increased a number of factors by which protein synthesis could be enhanced in the liver. It produced a 30% increase in the amount of ribosomes and mRNA per cell. The proportion of ribosomes associated with polysomes was increased by 5-10% over normal liver. There was a 10-30% increase in the rate of ploypeptide elongation and a small increase or no change in polysome size, indicating that the rate of polypeptide initiation was increased proportionately. The product of these effects accounts for the 1.5-fold increase in the rate of total protein synthesis previously reported. The average polysome size, and the size of free polysomes in particular, was maintained when actinomycin D was administered to phenobarbital-pretreated rats, suggesting that the rate of mRNA degradation was decreased selectively. Phenobarbital did not, however, affect the distribution of ribosomes between the free and membrane-bound states or the activity of ribonucleases associated with isolated free and bound polysomes. Thus, we conclude that phenobarbital stimulates protein synthesis by expanding the mRNA pool, at least partially through effects on mRNA degradation, and by augmenting the rate of mRNA translation.     

Nucleic-acid-templated synthesis as a model system for ancient translation

The translation of nucleic acids into synthetic structures with expanded functional potential has been the subject of considerable research, with applications including small-molecule and polymer evolution, reaction discovery and sensing. Here, we review properties of nucleic-acid-templated synthesis in the context of requirements for prebiotic translation. This analysis highlights the chemical possibilities of ancient translation systems, as well as challenges that these systems may have faced.     

Natural premature protein synthesis termination can be reduced in Escherichia coli by decreased translation rates.

Summary Peptidyl tRNA hydrolase is an essential enzyme for normal growth inasmuch as a mutant strain of Escherichia coli with a temperature-sensitive hydrolase cannot continue protein synthesis at the non-permissive temperature. In the absence of hydrolase peptidyl tRNA rapidly accumulates. Why peptidyl tRNA should be formed is the subject of this report. The rapid rate of protein synthesis is likely one mechanism of formation of peptidyl tRNA. A strA mutant of the hydrolase (pth-1) mutant strain that has a 40% reduction in amino acid polymerization rate can grow at 42° C. StrA mutants with normal polymerization rates, however, cannot grow at 42° C when pth-1 is present. Furthermore, addition of low levels of chloramphenicol (2–4 g/ml) but not several other tested drugs, phenotypically suppressed pth-1 at 42° C. Chloramphenicol, at these concentrations, was found to reduce the amino acid polymerization rate 30–40%. On the other hand, no evidence could be found that amino acyl tRNA selection errors are incorporated into pseudo revertants of the pth-1 strain.This investigation was supported by NSF grant No. PCM 76-11012. Journal Paper No. J-9502 of the Iowa Agriculture and Home Economics Experiment Station. Project No. 2299     

Purifying protein complexes for mass spectrometry: applications to protein translation

Proteins control and mediate most of the biological activities in the cell. In most cases, proteins either interact with regulatory proteins or function in large molecular assemblies to carryout biological processes. Understanding the functions of individual proteins requires the identification of these interacting proteins. With its speed and sensitivity, mass spectrometry has become the dominant method for identifying components of protein complexes. This article reviews and discusses various approaches to purify protein complexes and analyze the proteins using mass spectrometry. As examples, methods to isolate and analyze protein complexes responsible for the translation of messenger RNAs into polypeptides are described.     

Alcohol myopathy: impairment of protein synthesis and translation initiation

Alcohol consumption leads to numerous morphological, biochemical and functional changes in skeletal and cardiac muscle. One such change observed in both tissues after either acute alcohol intoxication or chronic alcohol consumption is a characteristic decrease in the rate of protein synthesis. A decrease in translation efficiency appears to be responsible for at least part of the reduction. This review highlights advances in determining the molecular mechanisms by which alcohol impairs protein synthesis and places these observations in context of earlier studies on alcoholic myopathy. Both acute and chronic alcohol administration impairs translational control by modulating various aspects of peptide-chain initiation. Moreover, this alcohol-induced impairment in initiation is associated with a decreased availability of eukaryotic initiation factor (eIF) 4E in striated muscle, as evidenced by an increase in the amount of the inactive eIF4E.4E-BP1 complex and decrease in the active eIF4E.eIF4G complex. In contrast, alcohol does not produce consistent alterations in the control of translation initiation by the eIF2 system. The etiology of these changes remain unresolved. However, defects in the availability or effectiveness of various anabolic hormones, particularly insulin-like growth factor-I, are consistent with the alcohol-induced decrease in protein synthesis and translation initiation.     

A cell-free protein synthesis system as an investigational tool for the translation stop processes

Using Escherichia coli cell-free protein synthesis system and aminoacylated amber suppressor tRNA, we successfully inserted an unnatural amino acid S-(2-nitrobenzyl)cysteine into human erythropoietin. Three different types of translation stop suppression were observed and each of the three types was easily discerned with SDS-PAGE. Optimal conditions were established for correct stop and programmed suppressions. Since this system differentiates proteins produced by misreading of codons from those produced by programmed suppression, we conclude that this cell-free translation system that we describe in this paper will be of a great use for future investigations on translation stop processes.     

A maximum likelihood framework for protein design

Background  

The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wider context, where additional constraints are captured by learning the sequence patterns displayed by natural proteins of known conformation. In this latter perspective, however, we still need a theoretical formalization of the question, leading to general and efficient learning methods, and allowing for the selection of fast and accurate objective functions quantifying sequence/structure compatibility.