Mechanism of protein biosynthesis

Metabolomic and metagenomic analyses of the Chinese mitten crab Eriocheir sinensis after challenge with Metschnikowia bicuspidata

Milky disease caused by Metschnikowia bicuspidata fungus has significantly harmed the Chinese mitten crab Eriocheir sinensis aquaculture industry. However, the effect of M. bicuspidata infection on the metabolism and intestinal flora of the crab remains unclear. In this study, we aimed to explore the changes in the metabolism and intestinal flora E. sinensis after 48 h of infection with M. bicuspidata, using metabolomic and metagenomic analyses. Metabolomic analysis results revealed 420 significantly different metabolites between the infected and control groups, and these metabolites were enriched in 58 metabolic pathways. M. bicuspidata infection decreased the levels of metabolites related to amino acid biosynthesis, the tricarboxylic acid cycle, as well as lysine, histidine, linolenic, arachidonic, and linoleic acid metabolism. These results indicated that M. bicuspidata infection significantly affected the energy metabolism, growth, and immunity of E. sinensis. The results of metagenomic analysis showed that the anaerobes and ascomycetes populations significantly increased and decreased, respectively, after M. bicuspidata infection. These changes in intestinal flora significantly upregulated metabolic and synthetic pathways while downregulating immunity-related pathways. The results of integrated metabolomic and metagenomic analyses showed that 55 differentially expressed genes and 28 operational taxonomic units were correlated with 420 differential metabolites. Thus, the intestinal flora changes caused by M. bicuspidata infection also affected the metabolites. This study provides novel insights into the metabolic-and intestinal microflora-based effects of M. bicuspidata infection in E. sinensis, as well as a theoretical basis for the interaction between fungi and crustaceans.

Multifaceted Design and Emerging Applications of Tissue Adhesives

Tissue adhesives can form appreciable adhesion with tissues and have found clinical use in a variety of medical settings such as wound closure, surgical sealants, regenerative medicine, and device attachment. The advantages of tissue adhesives include ease of implementation, rapid application, mitigation of tissue damage, and compatibility with minimally invasive procedures. The field of tissue adhesives is rapidly evolving, leading to tissue adhesives with superior mechanical properties and advanced functionality. Such adhesives enable new applications ranging from mobile health to cancer treatment. To provide guidelines for the rational design of tissue adhesives, here, existing strategies for tissue adhesives are synthesized into a multifaceted design, which comprises three design elements: the tissue, the adhesive surface, and the adhesive matrix. The mechanical, chemical, and biological considerations associated with each design element are reviewed. Throughout the report, the limitations of existing tissue adhesives and immediate opportunities for improvement are discussed. The recent progress of tissue adhesives in topical and implantable applications is highlighted, and then future directions toward next-generation tissue adhesives are outlined. The development of tissue adhesives will fuse disciplines and make broad impacts in engineering and medicine.

Physical and nutrient stimuli differentially modulate gut motility patterns, gut transit rate, and transcriptome in an agastric fish, the ballan wrasse

The effects of nutrient and mechanical sensing on gut motility and intestinal metabolism in lower vertebrates remains largely unknown. Here we present the transcriptome response to luminal stimulation by nutrients and an inert bolus on nutrient response pathways and also the response on gut motility in a stomachless fish with a short digestive tract; the ballan wrasse (Labrus berggylta). Using an in vitro model, we differentiate how signals initiated by physical stretch (cellulose and plastic beads) and nutrients (lipid and protein) modulate the gut evacuation rate, motility patterns and the transcriptome. Intestinal stretch generated by inert cellulose initiated a faster evacuation of digesta out of the anterior intestine compared to digestible protein and lipid. Stretch on the intestine upregulated genes associated with increased muscle activity, whereas nutrients stimulated increased expression of several neuropeptides and receptors which are directly involved in gut motility regulation. Although administration of protein and lipid resulted in similar bulbous evacuation times, differences in intestinal motility, transit between the segments and gene expression between the two were observed. Lipid induced increased frequency of ripples and standing contraction in the middle section of the intestine compared to the protein group. We suggest that this difference in motility was modulated by factors [prepronociceptin (pnoca), prodynorphin (pdyn) and neuromedin U (nmu), opioid neurotransmitters and peptides] that are known to inhibit gastrointestinal motility and were upregulated by protein and not lipid. Our findings show that physical pressure in the intestine initiate contractions propelling the bolus distally, directly towards the exit, whereas the stimuli from nutrients modulates the motility to prolong the residence time of digesta in the digestive tract for optimal digestion.

Wanderings in biochemistry

My Ph.D. thesis in the laboratory of Severo Ochoa at New York University School of Medicine in 1962 included the determination of the nucleotide compositions of codons specifying amino acids. The experiments were based on the use of random copolyribonucleotides (synthesized by polynucleotide phosphorylase) as messenger RNA in a cell-free protein-synthesizing system. At Yale University, where I joined the faculty, my co-workers and I first studied the mechanisms of protein synthesis. Thereafter, we explored the interferons (IFNs), which were discovered as antiviral defense agents but were revealed to be components of a highly complex multifunctional system. We isolated pure IFNs and characterized IFN-activated genes, the proteins they encode, and their functions. We concentrated on a cluster of IFN-activated genes, the p200 cluster, which arose by repeated gene duplications and which encodes a large family of highly multifunctional proteins. For example, the murine protein p204 can be activated in numerous tissues by distinct transcription factors. It modulates cell proliferation and the differentiation of a variety of tissues by binding to many proteins. p204 also inhibits the activities of wild-type Ras proteins and Ras oncoproteins.

A survey of polypeptide deformylase function throughout the eubacterial lineage

N-terminal formylation of ribosome-synthesized polypeptides is assumed to be among the most conserved features that distinguish the eubacterial line of descent from other living phyla. In order to assess the ancientness of this trait, def genes encoding polypeptide deformylase were characterized from four eubacterial species, Lactococcus lactis, Bacillus subtilis, Calothrix PCC7601 and Thermotoga maritima, taking advantage of the conditional viability of the def mutants of Escherichia coli. Altogether, eight sequences of polypeptide deformylase have been obtained from all the eubacterial sources which were investigated, either through systematic genome sequence analysis or through genetic screening, yielding a highly homologous family. A gene putatively encoding Met-tRNAi formyltransferase, fmt, was found downstream of the deformylase gene except in L. lactis, Mycoplasma genitalium, Calothrix PCC7601 and T. maritima. These results argue strongly for the ancestral character of N-terminal formylation in eubacteria. Most of the wide deviations of amino acid usage observed in def- and fmt-encoded proteins among species is best accounted for by the nucleotide composition of genomes. Furthermore, the species of origin of each protein appears to be more recognizable than its function, considering only its amino acid composition.

Effect of venom gland extracts of the South American brown spider, Loxosceles laeta, on in vitro protein synthesis

There was no effect of the venom extract on incorporation of phenylalanine into protein from phenylalanyl-tRNA. In contrast, the esterification of amino acids with tRNA was inhibited by the venom extracts in a dose-dependent manner, with an apparent preservation of the covalent structure of aminoacyl-tRNA.

Formylation of methionyl-transfer ribonucleic acid in Mycoplasma mycoides subsp. mycoides

Mycoplasma mycoides subsp. mycoides grows readily but does not formylate methionyl-transfer ribonucleic acid in a defined medium without an added formyl donor. Formylation occurs when the medium is supplemented with N5,N10-methenyltetrahydrofolate or N10-formyltetrahydrofolate, but not with folate.

Structural fluctuation of the polypeptide-chain elongation factor Tu. A comparison of factors from Escherichia coli and Thermus thermophilus HB8

The kinetics of hydrogen-deuterium exhcange in the polypeptide chain elongation factor Tu (EF Tu) from Escherichia coli and that from Thermus thermophilus HB8 has been examined in aqueous solutions at various pH and temperatures by means of infrared absorption measurements. The free EF-Tu from E. Coli has a greater reaction rate at all pH values and at every temperature than that of the GTP-bound or GDP-bound EF-Tu. The free EF-Tu from T. thermophilus, on the other hand, has an alomst equal reaction rate to that of EF-Tu-GDP in the temperature range 38-55 degrees C. For the peptide NH groups belonging to a medium-labile kinetic class, a small but definite difference in the rate of exchange reaction was observed between EF-Tu-GDP and EF-Tu-GTP for both E. coli and T. thermophilus. For less labile peptide NH groups, on the other hand, the rate of the exchange reaction with EF-Tu-GDP from T. thermophilus is only slightly affected by the pH of the solution at 38 degrees C and 45 degrees C, while the rate constant(k) with E. coli EF-Tu-GDP is pH-dependent (log k oc pH). For T. thermophilus EF-Tu, heat stability measurements, kinetics of the rates of GDP and GTP dissociation, and circular dichroic measurements have also been made. The molecular basis for the thermostability of T. thermophilus EF-Tu is discussed.

The interdependence of magnesium with spermidine and phosphoenolpyruvate in an enzyme-synthesizing system in vitro

The DNA-dependent syntheses of different enzymes of the bacteriophages T3 and T7 were studied in an Escherichia coli system in vitro with respect to the optimal Mg2+ concentration and its interdependence with substituting (e.g. spermidine) and complexing agents (e.g. phosphoenolpyruvate). The following results were obtained. 1. The optimal conditions for the syntheses of the different enzymes were not identical. The optima for RNA polymerase synthesis were 8 mM Mg2+, 10 mM P-pyruvate and 3 mM spermidine; for S-adenosyl-L-methionine cleaving enzyme synthesis, 6 mM Mg2+, 6 mM P-pyruvate and 3 mM spermidine; and for lysozyme synthesis, 13-18 mM Mg2+, 28 mM P-pyruvate and 3-0 mM spermidine. 2. The optimal conditions for the synthesis of analog enzymes (RNA polymerases and lysozymes) from the two templates were identical with experimental error. 3. Mg2+ and spermidine substituted for each other in relation to the number of their charges. 4. The apparent complexing of one Mg2+ molecule required the addition of 3-5 P pyruvate molecules. 5. Under the optimal conditions the enzyme-synthesizing activity was higher by more than a factor of 10 compared to previously described systems.

Translocation in Bacillus subtilis: characterization of elongation factor G by peptidyl-[3H]puromycin synthesis

This communication describes the characterization of elongation factor G from Bacillus subtilis by the translocation of "native" peptide donors. Translocation was followed by elongation factor G-dependent increase in the synthesis of peptidyl-[3H]puromycin using "washed" ribosomes carrying in vivo-bound peptidyl-transfer ribonucleic acid ("native" peptidyl-transfer ribonucleic acid) molecules as peptide donors. Such ribosomes were obtained from cell extracts by washing at a high salt concentration. The use of "native" peptide donors facilitated the study of translocation under conditions that are closer to the in vivo state than those in the methods previously employed.

Interaction of elongation factor Tu with 2'(3')-O-aminoacyloligonucleotides derived from the 3' terminus of aminoacyl-tRNA

The interaction between Escherichia coli elongation factor-Tu-GTP complex and chemically synthesized 2'(3')-O-aminoacyldinucleoside phosphates with the nucleotide sequence of the 3' terminus of aminoacyl-tRNA (AA-tRNA) has been studied. It was found that C-A-Phe, C-A-Pro, and C-A-Asp interact with EF-Tu-GTP, causing the release of GTP bound to the enzyme. The specificity of this interaction closely resembles that of AA-tRNA since C-A and C-A(Ac-Phe) as well as the corresponding tRNAs are inactive. The 3'-O-aminoacyl derivative C-2'-dA-Phe does not interact with EF-Tu-GTP, whereas the 2'-O-aminoacyl derivative C-3'-dA-Phe is almost as active as the 2'(3')-O-aminoacyl derivative, C-A-Phe. C-A-Phe also interacts with the EF-Tu-GDP complex in a manner similar to its interaction with EF-Tu-GTP. It is concluded that interaction of 2'(3')-O-aminoacyloligonucleotides possessing the sequence of the 3' terminus of AA-tRNA is analogous to the interaction of that terminus with EF-Tu and it is suggested that EF-Tu is specific for 2'-O-AA-tRNA.

Nucleotide composition analysis of tRNA from leukemia patient cell samples and human cell lines

A technique developed for analysis of less than microgram quantities of tRNA has been applied to the study of human leukemia. Leucocytes from peripheal blood and bone marrow samples of six, untreated leukemia patients and cells of five different established human cell lines were maintained for 18 hours in media containing (32P)-phosphate. Incorporation of radioactive phosphate into the cells from the patient samples was slightly less than that of the cell lines. Likewise, incorporation of (32P)-phosphate into the tRNA of the patient samples (approximately 5 x 106 DPM/mug tRNA) was also less then that incorporated into the tRNA of the cell lines. The major and minor nucleotide compositions of the unfractionated tRNA preparations from each patient sample and each cell line were determined and compared. Similarities and differences in the major and minor nucleotide compositions of the tRNA preparations are discussed with reference to types of leukemia and the importance of patient sample analysis versus analysis of cultured human cells.

An intercistronic region and ribosome-binding site in bacterial messenger RNA

A messenger RNA fragment about 220 nucleotides long has been isolated from 32-P-labeled tryptophan operon mRNA of Escherichia coli. When point mutations at the end of trpB and the beginning of trpA were introduced, the resulting nucleotide changes were found; hence the mRNA fragment must include the trpB-trpA intercistronic region. Most of the nucleotide sequences can be assigned to specific locations in the structural genes, based on the amino-acid sequences of the trpB and trpA proteins. In vitro, ribosomes bind to this piece of mRNA and protect from nuclease attack a region about 40 nucleotides long, containing a central AUG codon. The triplet codons to the 3' side of this AUG correspond to the first seven amino acids of the trpA protein; the codons to the 5' side correspond to the last six amino acids of the trpB protein. Translation of trpB is terminated by single UGA codon, which overlaps the trpA AUG initiation codon: UGAUG. Thus the untranslated "intercistronic" region consists of only two nucleotides. The RNA sequence spanning this region undoubtedly fulfills two functions, specifying ribosome recognition signals as well as encoding amino-acid sequences.

Methionine and formylmethionine specific tRNAs coded by bacteriophage T5

By RNA-DNA hybridization, as well as chemical and chromatographic analysis, evidence is provided that the bacteriophage T5 codes for the synthesis of two isoacceptor methionine transfer RNA species, tRNA-Met and tRNA-f-Met. Because of the differences in chromatographic properties of T5 phage and host methionine tRNAs, the phage tRNA species are readily distinguishable.

Defects of two temperature-sensitive lysyl-transfer ribonucleic acid synthetase mutants of Bacillus subtilis

Two temperature-sensitive mutants (lysS1 and lysS2) of the lysyl-transfer ribonucleic acid synthetase (l-lysine:tRNA ligase [adenosine 5'-monophosphate], EC 6.1.1.6) of Bacillus subtilis have been isolated. Although protein synthesis is inhibited in both mutants at the restrictive temperature (42 to 45 C), the mutants remain viable in a minimal medium. In comparison with the wild-type lysyl-tRNA synthetase, the l-lysine-dependent exchange of [(32)P]pyrophosphate with adenosine 5'-triphosphate (ATP) for both mutant enzymes is decreased. The lysS1 enzyme is completely defective in the ATP-dependent attachment of l-lysine to tRNA, whereas the lysS2 enzyme has 3- to 10-fold reduced levels of this activity. Temperature-resistant transformants have wild-type enzyme levels, whereas partial revertants to temperature resistance have varied levels of enzyme activity. The attachment and exchange activities of the lysS2 enzyme are more heat labile in vitro than the wild-type enzyme, as is the attachment activity of a partial revertant of the lysS1 mutant. The lysS1 and the lysS2 lysyl-tRNA synthetases have higher apparent K(m) values for lysine and ATP, in both the activation and the attachment reactions. The lysS2 enzyme has a V(max) for tRNA(lys) one-third that of the wild-type enzyme. Molecular weights of approximately 150,000 for the wild-type and lysS2 enzymes and approximately 76,000 for the lysS1 enzyme were estimated from sedimentation positions in sucrose density gradients assayed by the ATP-pyrophosphate exchange activity. We propose that the two mutations (lysS1 and lysS2) directly affect the sites for exchange activity, but indirectly alter attachment activity as a consequence of defective subunit association.

Studies of ribosomal diffusion coefficients using laser light-scattering spectroscopy

Using an optical beating technique, the diffusion coefficients and relative scattered intensity of Escherichia coli 70S, 50S, and 30S ribosomes are measured as a function of temperature and Mg(2+) concentration. For solutions at 10 mM Mg(2+) and between 0 degrees C and about 40 degrees C, the values of D(20,w) obtained are 1.7, 1.9, and approximately 2.1 x 10(-7) cm(2)/s, respectively. Preparative procedures drastically affect these values and equivalent hydrodynamic ellipsoids of revolution models give large axial ratios indicating extensive hydration or a deviation from the assumed shape. Calculations also indicate that the subunits expand upon dissociation. Measurements of D(20,w) vs. temperature indicate that 70S particles undergo a conformational change prior to dissociation and can be heat dissociated at 30-32 degrees C at low concentrations. Treatment of 70S ribosomes with EDTA causes a biphasic dissociation reaction. Addition of Mg(2+) after dissociation with EDTA shows that longer waiting times yield fewer 70S particles and that even short waiting times may yield ribosomes differing from the native conformation. Addition of p-chloromercuribenzoic acid (PCMB) is shown to dissociate 70S particles, but to a lesser extent than ethylenediaminetetraacetic acid (EDTA).

Initiation of protein synthesis by folate-sufficient and folate-deficient Streptococcus faecalis R: partial purification and properties of methionyl-transfer ribonucleic acid synthetase and methionyl-transfer ribonucleic acid formyltransferase

The initiation of protein synthesis by Streptococcus faecalis R grown in folate-free culture occurs without N-formylation or N-acylation of methionyl-tRNA(f) (Met). Methionyl-tRNA synthetase and methionyl-tRNA formyltransferase were partially purified from S. faecalis grown under normal culture conditions in the presence of folate (plus-folate); the general properties of the enzymes were determined and compared with the properties of the enzymes purified from wild-type cells grown in the absence of folate (minus-folate). S. faecalis methionyl-tRNA synthetase displays optimal activity at pH values between 7.2 and 7.8, requires Mg(2+), and has an apparent molecular weight of 106,000, as determined by gel filtration, and 127,000, as determined by sucrose density gradient centrifugation. The K(m) values of plus-folate methionyl-tRNA synthetase for each of the three substrates in the aminoacylation reaction (l-methionine, adenosine triphosphate, and tRNA) are nearly identical to the respective substrate Michaelis constants of minus-folate methionyl-tRNA synthetase. Furthermore, both plus- and minus-folate S. faecalis methionyl-tRNA synthetases catalyze, at equal rates, the aminoacylation of tRNA(f) (Met) and tRNA(m) (Met) isolated from either plus-folate or minus-folate cells. S. faecalis methionyl-tRNA formyltransferase displays optimal activity at pH values near 7.0, is stimulated by Mg(2+), and has an apparent molecular weight of approximately 29,900 when estimated by sucrose density gradient centrifugation. The K(m) value of plus-folate formyltransferase for plus-folate Met-tRNA(f) (Met) does not differ significantly from that of minus-folate formyltransferase for minus-folate Met-tRNA(f) (Met). Both enzymes can utilize either 10-formyltetrahydrofolate or 10-formyltetrahydropteroyltriglutamate as the formyl donor; the Michaelis constant for the monoglutamyl pteroyl coenzyme is slightly less than that of the triglutamyl pteroyl coenzyme for both transformylases. Tetrahydrofolate and uncharged tRNA(f) (Met) are competitive inhibitors of both plus- and minus-folate S. faecalis formyltransferase; folic acid, pteroic acid, aminopterin, and Met-tRNA(m) (Met) are not inhibitory. These results indicate that the presence or absence of folic acid in the culture medium of S. faecalis has no apparent effect on either methionyl-tRNA synthetase or methionyl-tRNA formyltransferase, the two enzymes directly involved in the formation of formylmethionyl-tRNA(f) (Met). Therefóre, the lack of N-formylation of Met-tRNA(f) (Met) in minus-folate S. faecalis is due to the absence of the formyl donor, a 10-formyl-tetrahydropteroyl derivative. Although the general properties of S. faecalis methionyl-tRNA synthetase are similar to those of other aminoacyl-tRNA synthetases, S. faecalis methionyl-tRNA formyltransferase differs from other previously described transformylases in certain kinetic parameters.

Requirement of initiation factor 3 in the initiation of polypeptide synthesis with N-acetylphenylalanyl-tRNA

Initiation factor 3 is required, along with initiation factors 1 and 2, for the incorporation of N-acetylphenylalanine into polypeptides and the formation of N-acetylphenylalanylpuromycin. Initiation factor 3 also strongly stimulates the binding of N-acetylphenylalanyl transfer RNA to isolated 30S ribosomal subunits. Phosphocellulose fractions of initiation factor 3 were found to catalyze N-acetylphenylalanine incorporation differentially with different synthetic messenger RNAs not containing any codons for N-formylmethionine. The results suggest that ribosomes recognize the initiator codon only through the initiator transfer RNA.

Magic spot metabolism in an Escherichia coli mutant temperature sensitive in elongation factor Ts

A temperature-sensitive mutant of Escherichia coli HAK88 which has been shown to have a lesion in elongation factor Ts (EFTs) was studied with repsect to its metabolism of guanosine 5'-diphosphate, 2'(3')-diphosphate (ppGpp) and the associated failure of ribosomal ribonucleic acid (rRNA) accumulation at the nonpermissive temperature. Results reported here show that (i) when EFTs is nonfunctional, a full complement of charged transfer RNA (tRNA) cannot prevent accumulation of ppGpp (magic spot) and the stringent failure of rRNA accumulation; (ii) chloramphenicol prevents magic spot (MS) formation and the stringent response not by increasing the percentage of charged tRNA, but possibly by somehow interfering directly with the synthesis of MS; and (iii) tetracycline can lead to MS disappearance without resumption of RNA synthesis. Thus, the absence of MS and the presence of a functional RNA polymerase and charged tRNA are not sufficient to support rRNA accumulation in vivo. An additional element in the regulatory system is suggested.

Peptide mapping of aminoacyl-tRNA synthetases: evidence for internal sequence homology in Escherichia coli leucyl-tRNA synthetase

Most aminoacyl-tRNA synthetases contain polypeptide chains of about either 50,000 or 100,000 daltons. Peptide mapping of tryptic, chymotryptic, or Staphylococcus aureus acid protease digests of seryl-tRNA synthetase (100,000, dimer) and leucyl-tRNA synthetase (100,000, monomer) from E. coli was done after selective modification of lysine residues with [(14)C]succinic anhydride or of methionine residues with [(14)C]iodoacetate. By use of thin-layer electrophoresis and chromatography on silicagel or cellulose plates followed by radioautography it was possible, depending upon the specific activity of the reagent used, to detect radioactive peptides obtained from as little as l mug of protein.Seryl-tRNA synthetase gave the correct number of tryptic peptides expected for a dimer of identical subunits. Leucyl-tRNA synthetase, on the other hand, gave roughly half the number of radioactive tryptic, chymotryptic, and acid protease peptides expected from the lysine, arginine, and methionine content of the 100,000 monomer. We have interpreted these results as indicating that extensive internal homology exists among lysine- and methionine-containing peptides within the leucyl-tRNA synthetase. The simplest conclusion that can be drawn from these observations is that the NH(2)- and COOH-terminal halves of leucyl-tRNA synthetase and perhaps other synthetases of 100,000 molecular weight may have evolved through a process of gene duplication and fusion, followed by limited diversification by way of amino-acid substitutions accumulating during evolution.

Reinitiation of a lac repressor fragment at a codon other than AUG

52 Spontaneous nonsense mutants in the lac i gene of Escherichia coli were isolated and characterized. All mutants located early in the gene show negative complementation in vivo with a wild-type i gene in a recA diploid strain. In vitro studies show that those mutants that display negative complementing activity in vivo also make lac repressor fragments retaining inducer binding and immunological crossreactivity with wild-type repressor. Amino-acid sequence analysis of these fragments shows that they arise by reinitiation at internal sities of the i message after chain termination at a prior amber or ochre codon. There are at least two different internal reinitiation sites in the first 200 nucleotides of the translated part of the i message. The first site corresponds to the first internal in phase AUG codon, which specifies the methionine residue at position 42 of the repressor protein. This site can be activated by an amber codon, 45 nucleotides before the AUG codon. The second site is only 60 nucleotides past the first site and can be activated by an amber mutation derived from residue 60 of the protein. The second initiation codon specifies the amino-acid leucine in the wild-type repressor, but the reinitiated fragment shows an amino-terminal methionine residue at this position. Therefore, the second initiation site seems to involve an in vivo ambiguity of the genetic code in that the same codon can be translated into two different amino acids depending on the recognition of this codon during initiation (when methionine is inserted) or elongation of protein synthesis (when leucine is inserted). The possibility that a codon other than AUG can act as an initiation codon in vivo is discussed.

NH2-terminal amino acid distribution and amino acid composition of Streptococcus faecalis R soluble and ribosomal proteins

The NH(2)-terminal amino acid distribution of Streptococcus faecalis R soluble and ribosomal proteins isolated from cells at different stages of growth on either folate-sufficient or folate-deficient medium was determined by the dinitrophenyl method. The NH(2)-terminal residues do not follow the random distribution observed for the total amino acid composition of S. faecalis soluble and ribosomal proteins. Methionine and alanine occur most frequently; serine, threonine, aspartic and glutamic acids, and glycine are also present at the NH(2)-terminal position of S. faecalis R proteins. The absence of folic acid yields cells that are incapable of formylating methionyl-transfer ribonucelic acid tRNA(f) (Met), but does not affect either the qualitative or quantitative NH(2)-terminal distribution of total soluble or total ribosomal proteins compared to cells grown with folate. A small quantitative difference was observed in the frequency of distribution of certain amino acids at the NH(2)-termini between log and stationary phase soluble proteins. The amino acid residues found at the NH(2)-terminal position of S. faecalis proteins are qualitatively similar to those reported for several other organisms.

The presence of N-terminal methionine on nascent protein of rat liver and rabbit reticulocytes and its cleavage during polypeptide-chain elongation

1. The size of nascent globin peptides from which the N-terminal methionine residue is cleaved has been investigated by comparing the proportion of N-terminal methionine and valine in short and long chains. Nascent chains were labelled in rabbit reticulocyte lysates, fractionated according to length by chromatography on Sephadex G-50, and analysed by the Edman degradation of selected pooled fractions. It was found that different peptide fractions contained either methionine or valine, but not both, as the N-terminal residue. Methionine was present at the N-terminus of globin chains containing up to approx. 50 amino acids whereas valine was found to be the N-terminal amino acid of longer peptides. 2. In similar experiments with nascent proteins of rat liver, labelled either in vivo or in a cell-free system containing microsomal material and cell sap, evidence was obtained for the presence of methionine at the N-terminus of nascent chains up to approx. 65 amino acid residues long. Thus protein synthesis in liver appears to be initiated also by methionine, but in this case cleavage takes place somewhat later during peptide elongation than in globin synthesis.

Assembly of bacterial ribosomes

I have not mentioned the remarkable progress made mainly by Fellner and his co-workers (86) in the elucidation of the primary structure of rRNA's and by Wittmann and his co-workers (87) in determining the structure of several ribosomal proteins. Such knowledge of primary structures is certainly the basis of complete understanding of the structure of the ribosome. With the current progress in technology, complete elucidation of the primary structure of all the ribosomal components is probably a matter of time. As indicated in this article, a rough approximation of the three-dimensional structure of ribosomes is likely to emerge soon. Although not mentioned in this article, studies of ribosomes from higher organisms are also progressing. We must, therefore, consider what further studies should be conducted and what kinds of questions we would like to solve. Some groups of investigators aim to elucidate the complete three-dimensional structure of ribosomes and to find out how these complex cell organelles function; they hope to determine the conformational changes of many of the component molecules within the ribosome structure in response to external macromolecules and cofactors engaged in protein synthesis. Such knowledge will also be important in enabling us to understand the regulation of translation of genetic messages. Other groups of investigators aim to elucidate the complex series of events which originate in the transcription of the more than 60 genes and culminate in the formation of the specific structure of the organelle. Complete reproduction in vitro of all the assembly events that occur in vivo should not be difficult to achieve in principle. It should then become possible to study in vitro any factor regulating the biogenesis of the organelle. Although we do not know whether such studies would reveal any new fundamental principle that governs the complex circuits of interconnected macromolecular interactions, the achievement of such a complete in vitro system would represent a necessary step in the comprehensive understanding of biogenesis of organelles, and eventually, of the more complex behavior and genesis of cells (89).

Isolation and characterization of a regulatory mutant of an aminoacyl-transfer ribonucleic acid synthetase in Escherichia coli K-12

From Escherichia coli strain K28, which is temperature sensitive for growth because of a mutation in its seryl-transfer ribonucleic acid (tRNA) synthetase gene (serS), temperature-resistant mutants were selected which were found to have a fivefold higher level of seryl-tRNA synthetase than the parent strain. The "high-level" character was found to be genetically stable and is due to a mutation in a locus denoted serO. This locus was found to be very closely linked to serS on the genetic map, and the relative gene order was concluded to be serS-serO-serC. In a serO(-) strain, the normal dependence of seryl-tRNA synthetase (SerRS) activity on changes of exogenous serine concentration was not observed. In a stable heterozygous merodiploid, the serO(-) mutation is still expressed, i.e., it is cis dominant. These results strongly suggest that serO is an operator site involved in the control of the serS gene.