Position of protein S1 in the 30 S ribosomal subunit of Escherichia coli

The results of neutron distance measurement involving ribosomal protein S1 from Escherichia coli are reported. These data provide a position for S1 on the small ribosomal subunit. They also indicate that S1, bound to the ribosome, has a radius of gyration of 60 to 65 Å, suggesting that its axial ratio in the bound state is similar to that it has as a free molecule in solution; namely, 10: 1. The implications of these results for our understanding of the mode of action of S1 are discussed.     

Interaction of ribosomal proteins S6, S8, S15 and S18 with the central domain of 16 S ribosomal RNA from Escherichia coli

The co-operative interaction of 30 S ribosomal subunit proteins S6, S8, S15 and S18 with 16 S ribosomal RNA from Escherichia coli was studied by (1) determining how the binding of each protein is influenced by the others and (2) characterizing a series of protein-rRNA fragment complexes. Whereas S8 and S15 are known to associate independently with the 16 S rRNA, binding of S18 depended upon S8 and S15, and binding of S6 was found to require S8, S15 and S18. Ribonucleoprotein (RNP) fragments were derived from the S8-, S8/S15- and S6/S8/S15/S18-16 S rRNA complexes by partial RNase hydrolysis and isolated by electrophoresis through Mg2+-containing polyacrylamide gels or by centrifugation through sucrose gradients. Identification of the proteins associated with each RNP by gel electrophoresis in the presence of sodium dodecyl sulfate demonstrated the presence of S8, S8 + S15 and S6 + S8 + S15 + S18 in the corresponding fragment complexes. Analysis of the rRNA components of the RNP particles confirmed that S8 was bound to nucleotides 583 to 605 and 624 to 653, and that S8 and S15 were associated with nucleotides 583 to 605, 624 to 672 and 733 to 757. Proteins S6, S8, S15 and S18 were shown to protect nucleotides 563 to 605, 624 to 680, 702 to 770, 818 to 839 and 844 to 891, which span the entire central domain of the 16 S rRNA molecule (nucleotides 560 to 890). The binding site for each protein contains helical elements as well as single-stranded internal loops ranging in size from a single bulged nucleotide to 20 bases. Three terminal loops and one stem-loop structure within the central domain of the 16 S rRNA were not protected in the four-protein complex. Interestingly, bases within or very close to these unprotected regions have been shown to be accessible to chemical and enzymatic probes in 30 S subunits but not in 70 S ribosomes. Furthermore, nucleotides adjacent to one of the unprotected loops have been cross-linked to a region near the 3' end of 16 S rRNA. Our observations and those of others suggest that the bases in this domain that are not sequestered by interactions with S6, S8, S15 or S18 play a role involved in subunit association or in tertiary interactions between portions of the rRNA chain that are distant from one-another in the primary structure.(ABSTRACT TRUNCATED AT 400 WORDS)     

Base-pairing between distant regions of the Escherichia coli 16 S ribosomal RNA in solution.

Intramolecular crosslinks have been introduced into Escherichia coli 16 S ribosomal RNA in aqueous solution by irradiation in the presence of hydroxymethyl-trimethylpsoralen. When the crosslinked RNA is denatured and examined in the electron microscope the most striking features are a variety of large open loops. In addition, because the crosslinked molecules are shortened compared to non-crosslinked molecules, there are likely to be small hairpins not resolved by the present technique. The sizes and positions of 11 loop classes have been determined and oriented on the molecule. The frequency of occurrence of the different classes of loops depends on the crosslinking conditions. When the crosslinking is done in solutions containing Mg²⁺, at least four of the loop classes appear with greater frequency than they do in 3.5 mm-NaCl. The loops presumably arise because complementary sequences separated by long intervening regions are being crosslinked. These base-pairing interactions between residues distant in the primary structure appear to be prominent features of the secondary structure of rRNA in solution.     

Intermediates of chromosomal DNA replication in Escherichia coli

The product of bacteriophage T4 gene 63 has two activities, one which catalyzes the attachment of tail fibers to base plates during morphogenesis (TFA) and one which catalyzes the joining of single-stranded polynucleotides (RNA ligase). The only phenotype attributed to mutations in gene 63 is a defect in attachment of tail fibers leading to fiberless T4 particles. However, it is suspected that TFA and RNA ligase are unrelated activities of the same protein since they have very different requirements in vitro.We have isolated new mutants which have lost the RNA ligase but have retained the TFA activity of the product of gene 63. These mutants exhibit defects in T4 DNA replication and late gene expression in some strains of Escherichia coli. This work allows us to draw three conclusions: (1) the TFA and RNA ligase activities are unrelated functions of the gene 63 product making this the prototype for a protein which has more than one unrelated function; (2) the RNA ligase is probably involved in DNA metabolism rather than RNA processing as has been proposed: (3) the RNA ligase and polynucleotide 5′ kinase 3′ phosphatase of T4 perform intimately related functions.     

Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes: a proposal for a synonymous codon choice that is optimal for the E. coli translational system

The relative quantities of 26 known transfer RNAs of Escherichia coli have been measured previously (Ikemura, 1981). Based on this relative abundance, the usage of cognate codons in E. coli genes as well as in transposon and coliphage genes was examined. A strong positive correlation between tRNA content and the occurrence of respective codons was found for most E. coli genes that had been sequenced, although the correlation was less significant for transposon and phage genes. The dependence of the usage of isoaccepting tRNA, in E. coli genes encoding abundant proteins, on tRNA content was especially noticeable and was greater than that expected from the proportional relationship between the two variables, i.e. these genes selectively use codons corresponding to major tRNAs but almost completely avoid using codons of minor tRNAs. Therefore, codon choice in E. coli genes was considered to be largely constrained by tRNA availability and possibly by translational efficiency. Based on the content of isoaccepting tRNA and the nature of codon-anticodon interaction, it was then possible to predict for most amino acids the order of preference among synonymous codons. The synonymous codon predicted in this way to be the most preferred codon was thought to be optimized for the E. coli translational system and designated as the “Optimal codon”. E. coli genes encoding abundant protein species use the optimal codons selectively, and other E. coli genes, such as amino acid synthesizing genes, use optimal and “non-optimal” codons to a roughly equal degree. The finding that the frequency of usage of optimal codons is closely correlated with the production levels of individual genes was discussed from an evolutionary viewpoint.     

Detection of amino-terminal tryptophan in peptides and proteins using dansyl chloride

A sensitive method is described for the detection of amino-terminal tryptophan in peptides and proteins as the dansyl derivative. The use of the method is illustrated with a tetrapeptide and with the enzyme phospholipase C from Bacillus cereus. The method may also be applicable when internal tryptophanyl residues are encountered during dansyl-Edman manual sequencing of peptides and proteins.     

Replacement of the B protein requirement of the E. coli quinolinate synthetase system by chemically-generated iminoaspartate

Two proteins (A and B) from $\text{Escherichia}\text{,}\text{coli}$ are required for $\text{in}\text{,}\text{vitro}$ synthesis of the NAD⁺ precursor, quinolinate, from L-aspartate and dihydroxyacetone phosphate. The requirement for B protein and L-aspartate in this system can be replaced by millimolar concentrations of oxaloacetate and ammonia if they are added together. This finding supports the concept that the B protein (L-aspartate oxidase) functions to form iminoaspartate which is condensed with dihydroxyacetone phosphate by the A protein to form quinolinate.     

Genetic mapping and DNA sequence analysis of mutations in the polA gene of Escherichia coli

DNA polymerase I of Escherichia coli provides an excellent model for the study of template-directed enzymatic synthesis of DNA because it is a single subunit enzyme, it can be obtained in large quantities and the three-dimensional structure of the polymerizing domain (the Klenow fragment) has recently been determined (Ollis et al., 1985). One approach to assigning functions to particular portions of the structure is to correlate the altered enzymatic behavior of mutant forms of DNA polymerase I with the change in the primary sequence of the protein. Towards this end we have developed a rapid procedure for mapping any polA mutation to a region no larger than 300 base-pairs within the polA gene. Two series of polA deletion mutants with defined end-points were constructed in vitro and cloned into bacteriophage lambda. These phages can then be used to map precisely E. coli polA mutants. Twelve polA- alleles have been mapped in this way and for nine of them the nature of the mutational change has been determined by DNA sequence analysis. Two of the mutations, polA5 and polA6, which affect the enzyme-DNA interaction, provide evidence for the location of the DNA binding region on the polymerase three-dimensional structure.     

Letter: Unequal contribution to ribosomal assembly of both str alleles in Escherichia coli merodiploids and its relationship to the dominance phenomenon

Two Escherichia coli strains were constructed which are reciprocal diploids for the str locus and isogenic for this region of the chromosome (str^s/′F str^r and str^r/′Fstr³). During exponential growth the steady-state ribosomal pools of both merodiploids are comprised of about 90%, or more, of streptomycin-sensitive ribosomes. Little effect of allele position was found. A similar preponderance of sensitive 30 S subunits over those that are resistant has been found during limited subunit reconstitution when an equimolar mixture of ribosomal proteins from both phenotypes was initially present. The results indicate that the rates of 30 S subunit assembly of both phenotypes are different, and that the sensitive sub-units predominate over the resistant subunits, suggesting that the difference in biosynthetic rate may be the basis for the dominance of this phenotype in vivo. An explanation for some aspects of the physiology of str diploids have been suggested in terms of these findings.     

Changes in gene expression during myogenic differentiation: II. Identification of the proteins encoded by myotube-specific complementary DNA sequences

Changes in the pattern of protein synthesis during terminal differentiation of a mouse, myogenic cell line have been examined by two-dimensional gel analysis. In addition the the increase in messenger RNAs coding for the major contractile proteins, several other new proteins are expressed after cell fusion, together with the diminution or loss of proteins expressed in mononucleate cells. In the accompanying paper (Affara et al., 1980), analysis of rnRNA changes using fractionated complementary DNA probes showed that a new group of mRNAs enters the polysomes after cell fusion. To identify which proteins are coded by mRNAs represented in this myotube-specific complementary DNA, we have vised a combination of in vitro translation and sulphydryl chromatography. The results indicate a correspondence between many of the new proteins appearing after cell fusion and the mRNAs encoded by myotube-specific complementary DNA sequences. Included amongst these proteins are some of the contractile polypeptides.     

Uptake, retention, and efflux of Ca2+ by mitochondrial preparations from skeletal muscle

Functionally intact mitochondria, substantially free of contamination, were isolated from rabbit gastrocnemius muscle after protease digestion and their Ca2+-handling properties examined. When judged by their capacity to retain large Ca2+ loads and the magnitude of basal and Na+-stimulated Ca2+ effluxes, the most suitable isolation method was digestion of finely minced muscle in buffered isoosmotic KCl with low levels (0.4 mg/g) of trypsin or the bacterial protease nagarse, followed by differential centrifugation. Polytron disruption of skeletal muscle in both sucrose- and KCl-based media released mitochondria deficient in cytochrome c. Use of the divalent ion chelator EDTA rather than EGTA in the isolation medium sharply reduced Ca2+-dependent respiratory control and tolerance of the mitochondria to Ca2+ loads, probably by removing Mg2+ essential to membrane integrity. ADP-dependent respiratory control was not altered in mitochondria prepared in an EDTA-containing isolation medium. Purification of mitochondria on a Percoll density gradient did not improve their Ca2+-handling ability despite removal of minor contaminants. Mitochondria prepared by the protease method could accumulate micromole loads of Ca2+/mg while maintaining a low basal Ca2+ efflux. Addition of BSA to the assay medium slightly improved Ca2+ retention but was not essential either during isolation or assay. Ca2+-dependent state 3 respiration was maximal at pH 6.5-7.0 while respiratory control and Ca2+/O were optimal at pH 7.0-7.5. Neither Pi nor oxaloacetate induced Ca2+ release from loaded mitochondria when monitored for 30 min after ruthenium red addition. Na+-stimulated Ca2+ efflux had sigmoidal kinetics with a Hill coefficient of 3. Since skeletal muscle mitochondria can be isolated and assayed in simple media, functional deficiencies of mitochondria from diseased muscle are unlikely to be masked.     

Liver microsomal polypeptides from Fischer-344 rats affected by age,sex, and xenobiotic induction

In order to investigate age and sex as determinants of hepatic cytochromes P-450, the polypeptide compositions of liver smooth microsomes from Fischer-344 rats were examined using two-dimensional gel electrophoresis (G. P. Vlasuk and F. G. Walz, Jr. (1980)Anal. Biochem. 105, 112). The effects of phenobarbital and 3-methylcholanthrene treatments were investigated using sexually immature (1 month), young adult (3 months), middle aged (12 months), and senescent (26 months) animals of both sexes. The appearance of five major microsomal polypeptides characterized sexual maturation in males. The only qualitative difference in the patterns of xenobiotic-induced polypeptides were found for young adult and middle-aged males where cytochrome P-450a (D. Ryan, P. E. Thomas, D. Korzeniowski, and W. Levin (1979)J. Biol. Chem. 254, 1365) was not induced by phenobarbital. A number of major microsomal polypeptides which might represent unidentified forms of cytochrome P-450 in untreated males and females were markedly decreased in a specific manner as a result of phenobarbital and/or 3-methylcholanthrene treatments. Microsomes from females of all ages tested and immature males were essentially indistinguishable on the basis of their total cytochrome P-450 contents and polypeptide patterns. Untreated senescent males were characterized by a reversion of their microsomal polypeptide patterns and total cytochrome P-450 contents to those for females and sexually immature males. In addition, phenobarbital-induced levels of total cytochrome P-450 for senescent males were the lowest observed for all of the groups tested even though their pattern of induced polypeptides was qualitatively the same as that for females.     

Modified two-dimensional electrophoresis for identification and autoradiography of ribosomal proteins reacted withp-chloromercuribenzoate

Ribosomal proteins labelled with [¹⁴C]PCMB, a reversibly reacting sulfhydryl reagent, lose most of their radioactivity when separated by the conventional two-dimensional polyacrylamide gel electrophoresis. Therefore, the two-dimensional method was modified to insure stability of the PCMB-protein complex during the procedure. Proteins ofEscherichia coli ribosomes were separated by the modified method, and those which reacted with [¹⁴C]PCMB were identified by counting of stained spots and by autoradiography of dried gels.     

Regulation of stable RNA synthesis and ppGpp levels in growing cells of Escherichia coli

Under the balanced condition of growth of E. coli cells, no distinct difference is observed in stable RNA and protein synthesis between CP78 (rel⁺) and CP79 (rel⁻), whereas a considerable difference is present in RNA accumulation between NF161 (rel⁺) and NF162 (rel⁻), where NF161 < NF162. The RNA content of NF161 is lower than that of NF162 in four different cultures with different growth rates. These two sets of isogenic pairs of rel⁺ and rel⁻ strains are commonly used in the study of rel gene function; however, NF161 is a mutant in the spoT gene whose product may be responsible for the degradation of ppGpp. The basal levels of ppGpp in these four strains growing with three different growth rates were examined: NF161 (rel⁺spoT⁻) has a much higher content of ppGpp than do other strains. Furthermore, the contents of ppGpp tend to be lower when the above four strains are growing at a faster rate. Thus a close correlation seems to exist between the content of RNA and the basal level of ppGpp under the condition of balanced growth.