A catalogue of transfer RNA-like molecules synthesized following infection of Escherichia coli by T-even bacteriophages

The discovery of a catalytic RNA within RNase P and its legacy

Sidney Altman's discovery of the processing of one RNA by another RNA that acts like an enzyme was revolutionary in biology and the basis for his sharing the 1989 Nobel Prize in Chemistry with Thomas Cech. These breakthrough findings support the key role of RNA in molecular evolution, where replicating RNAs (and similar chemical derivatives) either with or without peptides functioned in protocells during the early stages of life on Earth, an era referred to as the RNA world. Here, we cover the historical background highlighting the work of Altman and his colleagues and the subsequent efforts of other researchers to understand the biological function of RNase P and its catalytic RNA subunit and to employ it as a tool to downregulate gene expression. We primarily discuss bacterial RNase P-related studies but acknowledge that many groups have significantly contributed to our understanding of archaeal and eukaryotic RNase P, as reviewed in this special issue and elsewhere.

RNA processing and decay in bacteriophage T4

Bacteriophage T4 is the archetype of virulent phage. It has evolved very efficient strategies to subvert host functions to its benefit and to impose the expression of its genome. T4 utilizes a combination of host and phage-encoded RNases and factors to degrade its mRNAs in a stage-dependent manner. The host endonuclease RNase E is used throughout the phage development. The sequence-specific, T4-encoded RegB endoribonuclease functions in association with the ribosomal protein S1 to functionally inactivate early transcripts and expedite their degradation. T4 polynucleotide kinase plays a role in this process. Later, the viral factor Dmd protects middle and late mRNAs from degradation by the host RNase LS. T4 codes for a set of eight tRNAs and two small, stable RNA of unknown function that may contribute to phage virulence. Their maturation is assured by host enzymes, but one phage factor, Cef, is required for the biogenesis of some of them. The tRNA gene cluster also codes for a homing DNA endonuclease, SegB, responsible for spreading the tRNA genes to other T4-related phage.

The 3' CCACCA sequence of tRNAAla(UGC) is the motif that is important in inducing Th1-like immune response, and this motif can be recognized by Toll-like receptor 3

In this article, the immunogenicity of tRNA and the recognition of tRNA by Toll-like receptors (TLRs) are analyzed. Analyses of the effects of different tRNA(Ala)(UGC) fragments (tRNA(Ala)1-76 [corresponding to positions 1 through 76], tRNA(Ala)26-76, tRNA(Ala)40-76, tRNA(Ala)62-76, tRNA(Ala)1-70, tRNA(Ala)26-70, tRNA(Ala)40-70, and tRNA(Ala)62-70) on the immune responses of hepatitis B surface antigen (HBsAg) were performed with BALB/c mice. Results show that tRNA(Ala)1-76, tRNA(Ala)26-76, tRNA(Ala)40-76, and tRNA(Ala)62-76 adjuvants not only induced stronger T helper (Th) 1 immune responses but also cytotoxic-T-lymphocyte (CTL) responses relative to tRNA(Ala)1-70, tRNA(Ala)26-70, tRNA(Ala)40-70, and tRNA(Ala)62-70 adjuvants in HBsAg immunization. A deletion of the D loop (tRNA(Ala)26-76), anticodon loop (tRNA(Ala)40-76), or TpsiC (tRNA(Ala)62-76) loop of tRNA(Ala)(UGC) does not significantly decrease the adjuvant characteristic of tRNA(Ala)(UGC). However a deletion of the 3'-end CCACCA sequence (tRNA(Ala)1-70, tRNA(Ala)26-70, tRNA(Ala)40-70, and tRNA(Ala)62-70) of tRNA(Ala)(UGC) significantly decreased the adjuvant characteristic in Th1 and CTL immune responses. Moreover, the recognitions of different tRNA(Ala)(UGC) fragments by TLR3, TLR7, TLR8, and TLR9 were analyzed. Results show that a deletion of the 3' CCACCA sequence of tRNA(Ala)(UGC) significantly decreased the recognition by TLR3. We concluded that the 3' CCACCA sequence of tRNA(Ala)(UGC) is the important motif to induce Th1 and CTL responses and this motif can be effectively recognized by TLR3.

Evolution of T4-related phages

Much progress has been made in understanding T-even phage biology in the last 50 years. We now know the entire sequence of T4, encoding nearly 300 genes, only 69 of which have been shown to be essential under standard laboratory conditions; no specific function is yet known for about 140 of them. The origin of most phage genes is unclear, and only 42 genes in T4 have significant similarity to anything currently included in GenBank. Comparative analysis of related phages is now being used to gain insight into both the evolutionary origins and interrelationships of these phage genes, and the functions of their protein products. The genomes of phages isolated from Tbilisi hospitals, Long Island sewage plants, the Denver zoo, and Khabarovsk show basic similarity. However, these phages show substantial insertions and deletions in a number of regions relative to each other, and closer investigation of specific sequences often reveals much more complex relationships. There are only a few cases in T4-related phages in which there is evidence for evolution through DNA duplication. These include the fibrous products of genes 12, 34, and 37; head proteins gp23 and gp24; and the Alt enzyme and its downstream neighbors. T4 also contains 13 apparent relatives of group I and group II intron homing endonucleases. Distal portions of the tail fibers of various T-even phages contain segments closely related to tail-fiber regions of other DNA coliphages, such as Mu, P1, P2, and lambda. Horizontal gene transfer clearly emerges as a major factor in the evolution of at least the tail-fiber regions, where site-specific recombination probably is involved in the exchange of host-range determinants.

Valyl-tRNA synthetase modification-dependent restriction of bacteriophage T4

A strain of Escherichia coli, CP 790302, severely restricts the growth of wild-type bacteriophage T4. In broth culture, most infections of single cells are abortive, although a few infected cells exhibit reduced burst sizes. In contrast, bacteriophage T4 mutants impaired in the ability to modify valyl-tRNA synthetase develop normally on this strain. Biochemical evidence indicates that the phage-modified valyl-tRNA synthetase in CP 790302 is different from that previously described. Although the enzyme is able to support normal protein synthesis, a disproportionate amount of phage structural protein (serum blocking power) fails to mature into particles of the appropriate density. The results with host strain CP 790302 are consistent with either a gratuitous inhibition of phage assembly by faulty modification or abrogation of an unknown role that valyl-tRNA synthetase might normally play in viral assembly.

Processing of tRNA in prokaryotes and eukaryotes

Considerable progress has been made in defining the steps in the conversion of a tRNA precursor to a mature tRNA. These steps, which differ in different systems, include removal of precursor-specific residues from the 5' and 3' termini of the initial transcript, addition of the 3'-C-C-A terminus, splicing of intervening sequences, and modification of nucleotide residues. Despite these advances in defining the "pathways" of tRNA processing, relatively little is known about most of the enzymes actually involved in these processing steps. In this article I describe the sequence of reactions needed to convert the initial tRNA transcript to a functional, mature tRNA, and discuss the specificity and properties of enzymes known to be involved in this process. In addition, I speculate on the expected specificities of other enzymes involved in tRNA processing which have not yet been identified, and on the structural organization of the processing machinery.