Self cleavage of a precursor RNA from bacteriophage T4

We found that a precursor of an RNA molecule from T4-infected Escherichia coli cells (p2Spl; precursor of species 1) has the capacity to cleave itself in a specific position. This cleavage is similar to a cleavage carried out by the aid of a protein, RNase F, that has been previously identified. This cleavage could lead to the maturation of an RNA (species 1) found in T4-infected E. coli cells. The reaction is time and temperature-dependent and is relatively slow as compared to the protein-dependent reaction. It requires at least a monovalent cation and is aided by non-ionic detergents. In the absence of detergent the cleavage can occur but at a reduced rate. The substrate does not contain hidden nicks and a variety of experiments suggest that it does not contain a protein. Moreover, we found no indication that the cleavage is due to contaminating nucleases in the substrate or in the reagents. The intact secondary and tertiary structures of the molecule are necessary for the cleavage to occur. The finding of a self cleaving RNA molecule has interesting evolutionary implications.     

Three suppressor forms of bacteriophage T4 leucine transfer RNA

Three suppressor forms of bacteriophage T4 leucine transfer RNA were isolated and characterized. One suppresses U-A-G mutations, another suppresses U-A-G and U-A-A mutations, while the third suppresses U-G-A mutations. Each suppressor specifies a new anticodon sequence in leucine transfer RNA. Whereas wild-type leucine transfer RNA has the anticodon sequence N-A-A (N is a modified U), the suppressor forms have C-U-A, N-U-A or N-C-A, respectively.     

Biosynthesis of transfer RNA: isolation and characterization of precursors to transfer RNA in the posterior silkgland of Bombyx mori.

Distinct low molecular weight RNA species that have properties expected for the precursor to tRNA have been isolated from the posterior silkglands of the silkworm Bombyx mori. These RNAs migrate between 4 S and 5 S markers on acrylamide gels and are labeled preferentially in vivo in relation to tRNA. The precursor RNAs can be converted specifically into molecules indistinguishable in size from tRNA upon incubation with “cleavage” enzymes isolated from the silkgland ribosomes. Two of the three low molecular weight RNAs contain the modified residues, pseudouridine, dihydrouridine and ribothymidine, and are methylated in vivo, suggesting that these base modifications occur while the tRNA is still in its precursor stage.     

Asymmetric maturation of a dimeric transfer RNA precursor

Six of the eight transfer RNAs coded by bacteriophage T4 are synthesized via three dimeric precursor molecules. The sequences of two of these have been determined. Both of these precursors give rise to equimolar amounts of the cognate tRNA molecules in vivo. In contrast, even in wild-type infections, tRNA^Ile is present in ≤ 30% the amount of tRNA^Thr, with which it is processed from a common dimeric precursor.We have now determined the sequence of this dimer. In addition to the nucleotides present in tRNA^Thr and tRNA^Ile, it contains nine precursor-specific residues, located at the 5′ and 3′ termini and at the interstitial junction of the two tRNA sequences. While the three dimers share the majority of structural features in common, pre-tRNA^{Thr + Ile} is the only case in which an encoded tRNA 3′ -C-C-A terminus is present in the interstitial region.The processing of this dimer in various biosynthetic mutants has been analyzed in vivo and in vitro and shown to be anomalous in several respects. These results suggest that the apparent underproduction of tRNA^Ile can be explained by a novel processing pathway that generates a metabolically unstable tRNA^Ile product. Data from DNA sequence analysis of the T4 tRNA gene cluster (Fukada & Abelson, 1980) support the conclusion that the asymmetric maturation of this precursor is a consequence of the unique disposition of the -C-C-A sequence. These results argue that gene expression can be modulated at the level of RNA processing. The biological significance of this phenomenon is discussed in relation to evidence that tRNA^Ile has a unique physiological role.     

Structure of the RNA portion of the RNA-linked DNA pieces in bacteriophage T4-infected Escherichia coli cells.

A method for the isolation of the RNA portion of RNA-linked DNA fragments has been developed. The method capitalizes on the selective degradation of DNA by the 3′ to 5′ exonuclease associated with bacteriophage T4 DNA polymerase. After hydrolysis of the DNA portion, the RNA of RNA-linked DNA is recovered mostly as RNA tipped with a deoxyribomononucleotide and a small fraction as pure RNA. On the other hand, the 5′ ends of RNA-free DNA are recovered mostly as dinucleotides and a small fraction as mononucleotides.Using this method, we have isolated the primer RNA for T4 phage DNA synthesis. Nascent short DNA pieces were isolated from T4 phage-infected Escherichia coli cells and the 5′ ends of the pieces were dephosphorylated and then phosphorylated with polynucleotide kinase and [γ-³²P]ATP. After selective degradation of the DNA portions, [5′-³²P]oligoribonucleotides (up to pentanucleotide) were obtained with covalently bound deoxymononucleotides at their 3′ ends. More than 40% of the oligoribonucleotides isolated were pentanucleotides with pApC at the 5′-terminal dinucleotide. The 5′-terminal nucleotide of the tetraribonucleotides was AMP, but that of the shorter chains was not unique. The pentanucleotide could represent the intact primer RNA for T4 phage DNA synthesis.     

A small RNA that complements mutants in the RNA processing enzyme ribonuclease P

Four temperature-sensitive RNase P mutants were analyzed for the accumulation of 10 S RNA. In the 10 S region of the polyacrylamide gel two molecules appear, a and b. While the level of 10 Sa seems to be affected in some of the mutants, the 10 Sb molecule was not found in rnpB mutants. A plasmid (pL2), which contains Escherichia coli DNA sequences that complement, at least partially, rnp mutations, directs the synthesis of 10 Sb RNA. The presence of the pL2 plasmid complements the rnpA49, rnpB3187 and the rnpC241 mutations, as revealed by colony formation at “non-permissive” temperatures. However, the complementation of the rnpA49 mutation is much better than that of the other mutations. The complementation can also be measured by the increased level of RNase P activity in extracts. 10 Sa and b RNAs are unique among all RNAs tested thus far, since they are stable during exponential growth at 30 °C and 37 °C. However, at higher temperatures, such as 43 °C, the molecules are somewhat less stable, and they become rather labile when RNA synthesis is blocked by rifampicin. Structural analysis revealed that the 10 Sa and 10 Sb RNA molecules have dissimilar sequences.     

Construction and properties of a recombinant plasmid containing gene 32 of bacteriophage T4D

This paper describes the construction and characterization of a chimeric plasmid that encodes the single-stranded DNA-binding protein of bacteriophage T4D (the product of gene 32). The plasmid contains a 2·6 × 10³ base HindIII segment of T4 DNA that includes genes 59 and 32 as well as a portion of gene 33. Isolation of bacteria carrying the recombinant plasmid became possible when the segment of phage DNA contained an amber mutation in gene 32. This suggests that a functional gene 32 is deleterious to the cell. Using antibody to gene 32 protein, we have been able to demonstrate expression of the plasmid-borne gene 32 in uninfected bacteria. Deletion variants of the gene 32 plasmid have been constructed in vitro. These have been used to align the genetic map of the region with the restriction map and to study phage gene expression from the plasmid in both infected and uninfected cells. In phage-infected cells the level of functional gene 32 product regulates the efficiency of translation of its own messenger RNA. We also observe such self-regulation for gene 32 present on the plasmid.     

A restriction map of virulence plasmid pVYE439-80 from a serogroup 9 Yersinia enterocolitica strain

A restriction map of the virulence plasmid pVYE439-80, isolated from Yersinia enterocolitica 439-80 (serogroup 9) was constructed for EcoRI, BamHI, SstII, and SmaI. The mapping was done after cloning of about two-thirds of the plasmid in Escherichia coli. The restriction pattern was compared to those obtained with plasmids isolated from Y. enterocolitica strains of serogroups 1, 3, and 5b. The restriction sites are particularly conserved in a region of about 25 kb. This region contains fragments that are also conserved in serogroup 8 strains [J. Heeseman, C. Keller, R. Morawa, N. Schmidt, H. J. Siemens, and R. Lauf (1983) J. Infect. Dis. 147, 107-115] and that were shown, in strains from this serogroup, to encode calcium dependency [D. A. Portnoy, H. Wolf-Watz, I. Bolin, A. B. Beeder, and S. Falkow, (1984) Infect. Immun. 43, 108-114].     

Primary in vitro antibody response of rabbit lymphoid cells and T-B cell collaboration in the absence of detectable mitogens

To investigate whether the antibody response and T-B-cell collaboration in vitro can be obtained in the absence of mitogens, a method of obtaining an in vitro primary anti-sheep red blood cell antibody response by rabbit spleen and lymph node cells was developed. We used Marbrook culture vessels and a specially prepared medium containing 10% autologous serum and maintained at pH 7.4–7.6. The system was shown to be devoid of any polyclonal mitogens as assessed by [³H]thymidine incorporation and by direct examination for blast cells in stained smears. The primary response increased continuously over the 5-day cultivation period and only IgM but not IgG plaque-forming cells (PFC) were detected. In over 20 experiments, the response ranged from 357 ± 17 to 4425 ± 110 PFC/10⁷ cultured cells with a median stimulation index of 52. The spleen cells required less antigen than the lymph node cells and 2-mercaptoethanol inhibited the response of the spleen cells but not that of the lymph node cells. Lymphocytes were separated into highly pure T- and B-cell populations by negative selection using antibody-coated human erythrocytes to rosette either T or B cells and Ficoll-Hypaque centrifugation to remove rosetted cells. Upon cultivation, B cells alone gave a low IgM response, whereas B cells reconstituted with T cells gave a response similar to that obtained with unseparated lymphoid cells. We concluded that: (a) optimal conditions for obtaining primary in vitro antibody responses using rabbit spleen and lymph node cells were established, (b) T-B-cell collaboration was demonstrated in the rabbit primary antibody response to sheep erythrocytes, and (c) the primary antibody response in vitro and T-B-cell collaboration may occur in the absence of detectable polyclonal mitogens.     

Ribonucleoprotein organization of eukaryotic RNA. XXXI. Structure of the U1 small nuclear ribonucleoprotein

A small nuclear ribonucleoprotein, U1 snRNP, has been implicated in mRNA processing. In this investigation sites of protein binding on U1 RNA were mapped by nuclease protection and RNA sequencing. Partially purified human U1 snRNP was sequentially digested with Escherichia coli RNAase III and S1 nuclease. The resistant ribonucleoprotein fragments were deproteinized, preparatively hybridized to the U1 RNA--complementary DNA strand of a human U1 gene cloned in bacteriophage M13, and displayed by electrophoresis. The nuclease-resistant U1 RNA fragments were between 23 and 63 nucleotides in length. Most of these fragments were not obtained when protein-free U1 RNA was similarly digested, whereas others were obtained in low yield from U1 RNA and much higher yield from U1 snRNP. RNA sequencing of the fragments revealed that the protein-protected sites in U1 snRNP correspond to base-paired stems I and II, loop a, and portions of stems III and IV (secondary structure nomenclature of Branlant et al., 1981). Single, "bulged" pyrimidines are present within the protein-covered helical regions of stems I and III. Most interestingly, the single-stranded 5' end of U1 RNA, implicated in mRNA splicing, was also highly protected by protein. These results demonstrate that the great majority of U1 RNA is covered by protein in U1 snRNP. The association of protein with the 5' end of U1 RNA is in agreement with recent evidence that snRNP proteins potentiate the binding of this region of U1 RNA with pre-mRNA splice sites.     

Chemical and functional quantitation of gene 0·3 messenger RNA during T7 infection

Late in infection of Escherichia coli by bacteriophage T7 a discrepancy is observed between the sythesis of the early gene 0·3 protein in vivo and the level of 0·3 mRNA measured by both chemical and functional assays. Chemical 0·3 mRNA levels have been measured by competition hybridization using purified, radioactive 0·3 mRNA, and functional 0·3 mRNA levels have been measured by cell-free translation. These measurements indicate that functional and chemical 0·3 mRNA persists late in T7 infection; 0·3 mRNA inactivation or decay cannot account for the shut-off of 0·3 protein synthesis in vivo. In addition the rate of loss of 0·3 mRNA activity and the rate of chemical decay of 0·3 mRNA are very similar.     

Developmental studies of lethality associated with the antennapedia gene complex in Drosophila melanogaster

A number of dominant homoeotic mutations are localized to the proximal right arm of chromosome 3 of Drosophila melanogaster and are thought to represent members of a gene complex that controls normal determinative decisions in the head and thorax. We have designated this complex the Antennapedia gene complex (ANT-C). Developmental studies were done to investigate the nature of the lethality associated with members of two of the complementation groups within ANT-C. The first complementation group, represented by the mutant Multiple Sex Combs (Msc) is characterized by embryonic lethality when heterozygous with a deletion of the ANT-C. The second complementation group consists of Antennapedia (Antp), Antennapedia-Extra Sex Combs (Antp^Scx), and the lethals recovered as revertants of Antp^Ns. When heterozygous for a deletion of the ANT-C or in heterozygous condition with each other, the members of this group show effective lethal phases spanning from embryo-larval boundary to late larval stages. Wakimoto and Kaufman (1981) show that the Antp⁺ gene acts to establish normal determinative states in the thorax. In the present work, transplantation of eye-antennal disks from lethal individuals heterozygous for two different Antp^Ns revertant chromosomes into wild-type hosts allowed the assessment of the function of the Antp⁺ allele in the antenna. Since these transplants formed only antennal structures and showed no evidence of the antennal → leg transformation seen in Antp^Ns controls, we conclude that the wild-type function of the Antp locus is not necessary for the establishment and/or maintenance of the antennal determined state. We suggest that regulatory mechanisms associated with the Antp⁺ structural gene normally function both to allow its expression in the thorax and to repress it in the antenna.     

Heterocyst differentiation and tryptophan metabolism in the cyanobacterium Anabaena sp. CA

Anabaena sp. CA does not synthesize heterocysts or express nitrogenase activity when grown with nitrate as the nitrogen source. Heterocysts and nitrogenase are induced in such cultures by various tryptophan analogs. The effect does not require inhibition of de novo protein synthesis in the culture. It is restricted to tryptophan analogs only, and, more specifically, to those which can be incorporated into proteins. dl-7-Azatryptophan was effective at triggering both heterocysts and nitrogenase when incubated in the culture for only 1–2 h, even though 6–7 h was required for heterocysts to fully mature and nitrogenase activity to be expressed. Chloramphenicol completely negated this effect, supporting the idea that the analogs are either incorporated into protein themselves or trigger the synthesis of proteins which initiate complete development of mature heterocysts. Using toluene-permeabilized cells, we have shown that anthranilate synthetase, the first key enzyme in tryptophan biosynthesis, has glutamine-dependent activity. This activity can be effectively feedback inhibited by the various tryptophan analogs at concentrations which are also effective in triggering heterocyst differentiation. These data provide firm evidence for a link between tryptophan biosynthesis, nitrogenase synthesis, heterocyst differentiation, and primary ammonia assimilation.     

Fluorescent labeling of fragments of high molecular weight RNA.

We describe a method to fluorescently label microgram quantities of high molecularweight RNA with acriflavine. The method involves hydrolyzing the RNA with HCl at pH 1.0 for 10 min to obtain segments of about 80 nucleotides. The 3′-terminal phosphate is removed from the ribose with alkaline phosphatase, and the terminal ribose is oxidized with periodate to form dialdehydes. Acriflavine is bound to the dialdehyde by the formation of a Schiff's base, and unbound acriflavine is removed by dialysis followed by chromatography on a Sephadex G-25 column eluted with phosphate buffered guanidine-HCl. Human 18 S rRNA bound 0.94 acriflavine molecules per 100 nucleotides and had a fluorescence excitation maximum at 460 nm and an emission maximum at 508 nm. If the hydrolysis step was omitted, this RNA bound only 0.12 acriflavine molecule per 100 nucleotides. Acriflavine-labeled high molecular weight yeast RNA showed a fluorescent intensity which was proportional to RNA concentration to a 1000-fold dilution.     

T-independent but not T-dependent antigens maintain surface Ig of lymphocytes.

The effect of T-independent (TIA) and T-dependent (IDA) antigens on the surface Ig of 24-hr cultured rabbit spleen cells was investigated by two techniques: the proportion of cells bearing surface Ig was determined by direct rosette formation with anti-light chain allotype-coated erythrocytes; the total amount of surface Ig was estimated by labeling the cells with anti-allotype ¹²⁵I-labeled Fab fragments. The addition of TIA resulted in the maintenance of the proportion of Ig-bearing cells almost to the initial level, an effect which could not be obtained with any of the TDA tested. The same type of effect was observed when the total amount of surface Ig was measured, i.e., there was a slight reduction (about 24%) in the amount of surface Ig in cultures to which TIAs were added and an almost sixfold reduction (about 70%) in cultures to which TDA, Con A, or no antigen was added. Some but not all of the TIA were able to induce [³H]TdR incorporation in 3-day spleen-cell cultures. We concluded that the common feature of TIA is the ability to stimulate the turnover of B-cell surface Ig, a feature that can be used for an easy screening of TIA.