Preferred sites of digestion of a ribonuclease from Enterobacter sp. in the sequence analysis of Bacillus stearothermophilus 5S ribonucleic acid

Purification and characterization of ribonuclease M and mRNA degradation in Escherichia coli

A previously unreported endoribonuclease has been identified in Escherichia coli, which has a preference for hydrolysis of pyrimidine-adenosine (Pyd-Ado) bonds in RNA. It was purified about 7000-fold to give a single band after SDS/polyacrylamide gel electrophoresis; the eluted protein gave the same RNase specificity. The sizes of the native and denatured enzymes agreed suggesting that the enzyme exists as a monomer of approximately 26 kDa. It is called RNase M. The only other reported broadly specific endoribonuclease in E. coli is RNase I, a periplasmic enzyme. Based on differences in charge, heat stability and substrate specificity, it was clear that RNase M is not RNase I. The specificity of RNase M was remarkably similar to that of pancreatic RNase A even though the two enzymes differ in charge characteristics and size. Earlier studies had shown that mRNA from the lactose operon of E. coli is hydrolyzed in vivo primarily between Pyd-Ado bonds [Cannistraro et al. (1986) J. Mol. Biol. 192, 257-274] We propose that this major RNase activity accounts for these cleavages observed in vivo and that it is the endonuclease for mRNA degradation in E. coli.

Pyrimidine-specific cleavage by an endoribonuclease of Saccharomyces cerevisiae

An endoribonuclease with pyrimidine cleavage site specificity was isolated from Saccharomyces cerevisiae. The enzyme had a pH optimum of 6 to 7 and did not require a divalent cation. It was inhibited by 5 X 10(-5) M ethidium bromide, although it appeared to be single strand specific. The enzyme gave a limited cleavage of yeast mRNA and rRNA, yielding products that were terminated with pyrimidine nucleoside 2',3'-cyclic phosphate. The bonds between pyrimidine and A residues constituted more than 90% of the scission sites when the average product size was 50 nucleotides. Homopolyribonucleotides were cleaved poorly. Poly(A,U) was cleaved rapidly, and analysis of the products of poly(A,U) hydrolysis showed a very stringent cleavage of U-A bonds.

Peptides isolated from Enterobacter nuclease as potential polyamine binding sites

The Enterobacter nuclease, which cleaves RNA between the 3'-phosphate group of cytidylic acid and the 5'-hydroxyl group of adenylic acid, has been shown to be affected by the polyamines, spermidine, spermine and putrescine. These substances enhance the hydrolytic activity of the enzyme against both poly(C) and yeast RNA. Sperimidine and spermine also reverse the inhibition of the enzyme by the ordered polynucleotides, apparently by removing them from the surface of the enzyme. Treatment of poly(G)-bound peptides (obtained from tryptic digests of poly(G)-bound nuclease) with an excess of spermidine resulted in the isolation of spermidine-bound peptides. Purification of these peptides through ion-exchange chromatography resulted in the isolation of three spermidine-bound peptides which consisted of 17 residues (6 amino acids), 19 residues (10 amino acids), and 12 residues (9 amino acids). The binding ratio of spermidine to peptides varied from 1:1 to 3:1.

Frequency of insertion-deletion, transversion, and transition in the evolution of 5S ribosomal RNA

The problem of choosing an alignment of two or more nucleotide sequences is particularly difficult for nucleic acids, such as 5S ribosomal RNA, which do not code for protein and for which secondary structure is unknown. Given a set of 'costs' for the various types of replacement mutations and for base insertion or deletion, we present a dynamic programming algorithm which finds the optimal (least costly) alignment for a set of N sequences simultaneously, where each sequence is associated with one of the N tips of a given evolutionary tree. Concurrently, protosequences are constructed corresponding to the ancestral nodes of the tree. A version of this algorithm, modified to be computationally feasible, is implemented to align the sequences of 5S RNA from nine organisms. Complete sets of alignments and protosequence reconstructions are done for a large number of different configurations of mutation costs. Examination of the family of curbes of total replacements inferred versus the ratio of transitions/transversions inferred, each curve corresponding to a given number of insertions-deletions inferred, provides a method for estimating relative costs and relative frequencies for these different types of mutations.

Thermal denaturation of mesophilic and thermophilic 5S ribonucleic acids

The Tm of Bacillus stearothermophilus 5S ribonucleic acid (RNA) is 1.5 +/- 0.5 C higher than that of 5S RNAs from B. subtilis and Escherichia coli. Melting in 50% methanol and in formaldehyde indicate that both base stacking and helical regions are involved in the slightly increased thermal stability of B. stearothermophilus 5S RNA. It is probable that the 5S RNA makes only a minor contribution to the thermostability of B. stearothermophilus 50S ribosomal subunits.

Evolution of 5sRNA

The evolution of 5sRNA of 17 organisms ranging from human to bacteria has been studied using a sequence homology analysis. The evolutionary rate of 5sRNA genes has been estimated to be 2.2x10(-10) replacement per one nucleotide site per year. This value is about the same as that of cytochrome C or tRNA's (congruent to 2x10(-10)). A phylogenic tree of these organisms including both eukaryotes and prokaryotes has been constructed from the evolutionary distances (the rate of nucleotide substitution per site) data. The time of divergence of prokaryotes and eukaryotes was estimated to be greater than or congruent to 1.75x10(9) years ago and the branching order in eukaryotic kingdoms is consistent with the traditional order. Blue-green algae separated from the bacterial stem greater than or congruent to 1.3x10(9) years ago after eukaryotes had branched.

Sequence studies on the 5S RNA of Proteus vulgaris: comparison with 5S RNA of Escherichia coli

We have studied the sequence of 5S ribosomal RNA of Proteus vulgaris. Although several doubts remain, it seems that no more than 8 per cent of the nucleotides differ from those of Escherichia coli 5S RNA. Of the ten bases differing from Escherichia coli 5S RNA sequence, three changes take place in one of the six positions which are known as intercistronic mutation points in Escherichia coli 5S RNA. We can conclude that they are "hot spots" of mutation.

Nucleotide sequence of 5-S RNA from Bacillus licheniformis

The complete nucleotide sequence of 5-S RNA from Bacillus licheniformis was determined by analysis of complete and partial digests obtained with either T1 or pancreatic ribonuclease. The molecule was found to have a length of 116 nucleotides and may possess a minor sequence heterogeneity. There is a large degree of homology between the sequence of B. licheniformis 5-S RNA and those published for 5-S RNA from B. megatherium and B. stearothermophilus. The difference between the three 5-S RNA species are limited mainly to the two terminal and one internal sequence. B. licheniformis 5-S RNA contains the sequence U95-G-A-G-A-G100, which in B. subtilis has been implicated in the processing of precursor 5-S RNA. Possible models for the secondary structure of prokaryotic 5-S RNA are discussed on the basis of the results of limited digestion of B. licheniformis 5-S RNA by ribonuclease T1.

The architecture of 5S rRNA and its relation to function

An extensive comparative analysis of the available primary sequence data on 5S rRNA has been made. A universal secondary structure is presented for procaryotic 5S rRNA which contains four helical regions. Eucaryotic 5S rRNAs are found to have only three of these helices and thus have a somewhat different architecture. In addition, a highly conserved segment of more than thirty nucleotides is identified in the 5' half of the procaryotic molecule. This segment includes the oligonucleotide -CGAAC- which presumably binds to the t-RNA "common" sequence -GTpsiCG-. Among the eucaryotes, the plants display a procaryotic nature in this region, but no eucaryote has the sequence -CGAAC- in this segment. A functional role for the procaryotic 5S rRNA molecule is discussed in which it is envisioned to undergo conformational change, i.e., coiling and uncoiling of one of the helices, which can result in a cyclic interaction of the 5S rRNA molecule with two t-RNA molecules. A general principle also emerges: the natural rotational motion inherent in coiling and uncoiling of nucleic acid helices can be converted quite simply to linear mechanical motion.

The nucleotide sequence preceding an RNA polymerase initiation site on SV40 DNA. Part 1. The sequence of the late strand transcript

The nucleotide sequence of the transcript of the "late" strand of the region of SV40 DNA preceding the preferred initiation site for Escherichia coli RNA polymerase has been determined to be U-G-U-A-A-C-C-A-U-U-A-U-A-A-G-C-U-G-C-A-A-U-A-A-A-C-A-A-G-U-U-A-A-C-A-A-C-A-A-C-A-A-U-U-G-Cp. Hemophilus influenza restriction endonuclease cleaves this region 30 nucleotides (base pairs) before the site of initiation of RNA synthesis by RNA polymerase.

The nucleotide sequence preceding an RNA polymerase initiation site on SV40 DNA. Part 2. The sequence of the early strand transcript

The nucleotide sequence of the RNA transcript from the "early" (E) strand of SV40 DNA immediately preceding the preferred E. coli RNA polymerase start site is G-(A-A-A-C, -A-U-)-A-A-A-A-U-G-A-A-U-G-C-A-A-U-U-G-U-U-G-U-U-G-U-U-A-A-C-U-U-G-U-U-U-A-U-U-G-C-A-G-C-U-U-A-U-A-A-U-G-G-U-U-A-C-Ap. The last nucleotide of the sequence is the first nucleotide transcribed by E. coli RNA polymerase from the "E" strand. The DNA template contains a palindrome of 17 residues that includes the Hemophilus influenza restriction endonuclease cleavage site G-T-T-A-A-Cp. The DNA which gives this transcript lies very close to one end of SV40 DNA segment in the Adeno-SV40 hybrid virus Ad2+ND3 and appears to contain sufficient untranscribed information to specify the E. coli RNA polymerase start.