A comparison of rabbit liver and reticulocyte transfer RNA: evidence of unique species in reticulocytes

The Yin and Yang of codon usage

The genetic code is degenerate. With the exception of two amino acids (Met and Trp), all other amino acid residues are each encoded by multiple, so-called synonymous codons. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in genes/genomes suggested that codon choice might have functional implications beyond amino acid coding. The pattern of non-uniform codon use (known as codon usage bias) varies between organisms and represents a unique feature of an organism. Organism-specific codon choice is related to organism-specific differences in populations of cognate tRNAs. This implies that, in a given organism, frequently used codons will be translated more rapidly than infrequently used ones and vice versa A theory of codon-tRNA co-evolution (necessary to balance accurate and efficient protein production) was put forward to explain the existence of codon usage bias. This model suggests that selection favours preferred (frequent) over un-preferred (rare) codons in order to sustain efficient protein production in cells and that a given un-preferred codon will have the same effect on an organism's fitness regardless of its position within an mRNA's open reading frame. However, many recent studies refute this prediction. Un-preferred codons have been found to have important functional roles and their effects appeared to be position-dependent. Synonymous codon usage affects the efficiency/stringency of mRNA decoding, mRNA biogenesis/stability, and protein secretion and folding. This review summarizes recent developments in the field that have identified novel functions of synonymous codons and their usage.

Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity

Messenger RNA is a key component of an intricate regulatory network of its own. It accommodates numerous nucleotide signals that overlap protein coding sequences and are responsible for multiple levels of regulation and generation of biological complexity. A wealth of structural and regulatory information, which mRNA carries in addition to the encoded amino acid sequence, raises the question of how these signals and overlapping codes are delineated along non-synonymous and synonymous positions in protein coding regions, especially in eukaryotes. Silent or synonymous codon positions, which do not determine amino acid sequences of the encoded proteins, define mRNA secondary structure and stability and affect the rate of translation, folding and post-translational modifications of nascent polypeptides. The RNA level selection is acting on synonymous sites in both prokaryotes and eukaryotes and is more common than previously thought. Selection pressure on the coding gene regions follows three-nucleotide periodic pattern of nucleotide base-pairing in mRNA, which is imposed by the genetic code. Synonymous positions of the coding regions have a higher level of hybridization potential relative to non-synonymous positions, and are multifunctional in their regulatory and structural roles. Recent experimental evidence and analysis of mRNA structure and interspecies conservation suggest that there is an evolutionary tradeoff between selective pressure acting at the RNA and protein levels. Here we provide a comprehensive overview of the studies that define the role of silent positions in regulating RNA structure and processing that exert downstream effects on proteins and their functions.

The complement of cytoplasmic tRNAs, including queuosine-containing tRNAs, in adult and senescent Wistar rat liver and their levels of aminoacylation

Our previous studies showed that both total cytoplasmic tRNAs and aminoacyl-tRNA synthetases isolated from senescent (24-30 month) female Wistar rat liver were less capable of supporting cell-free protein synthesis than were the same fractions isolated from adult (10-13 month) rat liver. The present study investigates the molecular basis for this age-related result. No significant age-related differences were found in the extent of aminoacylation of the liver cytoplasmic tRNA population, the total tRNA synthetase activity, the rate of aminoacylation of individual tRNAs, or in the overall complement of tRNA species as detected by two-dimensional gel electrophoresis. In homologous senescent aminoacylation assays, consisting of tRNAs and tRNA synthetases from senescent animals, alanine, arginine and aspartic acid were charged to a greater extent and methionine to a lesser extent compared to homologous adult assays. In heterologous assays, adult synthetases were significantly more active than senescent synthetases when charging isoleucine, methionine, phenylalanine, proline and glutamic acid, and less active when charging alanine, aspartic acid and serine. Also, senescent synthetases charged both adult and senescent tRNAs with methionine to a lesser extent than did adult synthetases. In homologous senescent assays with queuosine-containing tRNAs, asparagine, aspartic acid and histidine were charged to a greater extent and tyrosine to a lesser extent compared to homologous adult assays. Results with queuosine-tRNAs are discussed in terms of their potential ability to lower the efficiency of translation in senescent liver.

Isoacceptor glycine tRNA species during bovine myocardium development

The isoacceptor patterns of glycyl-tRNAs from fetal bovine myocardium during development, and of adult cardiac muscle, have been studied by reverse-phase chromatography. 4 isospecies were detected and quantitative changes in their relative abundance were noted. Moreover, upon testing their efficiency in transferring glycine into polypeptides a differential utilization of the cognate tRNAs was observed.

Aminoacyl-transfer RNA populations in mammalian cells chromatographic profiles and patterns of codon recognition

The chromatographic profiles of 20 aminoacyl-tRNAs from rabbit liver were compared to those of rabbit reticulocytes by reverse phase chromatography and the chromatographic profiles of 20-aminoacyl-tRNAs from bovine liver were compared to those of bovine brain. The two rabbit tissues showed significant differences in the elution profiles of most aminoacyl-tRNAs, while the elution profiles of the aminoacyl-tRNAs from the bovine tissues showed fewer differences. The patterns of codon recognition of several aminoacyl-tRNAs fractionated from rabbit reticulocytes have also been compared to those fractionated from rabbit liver.

The primary structure of rabbit beta-globin mRNA as determined from cloned DNA

The rabbit beta-globin DNA insertion of the hybrid plasmid PbetaG1 (Maniatis et al., 1976) was sequenced by the method of Maxam and Gilbert (1977). A sequence of 576 nucleotides was determined and verified by pyrimidine tract analysis of double-stranded DNA, synthesized in vitro starting from beta-globin mRNA. The derived sequence is in complete agreement with previously reported partial mRNA sequencing data and with the predictions from the primary structure of the protein. Moreover, the globin DNA insertion is missing only 13 nucleotides corresponding to the 5' terminal sequence of the mRNA. The rabbit beta-globin mRNA consists of a coding region of 438 nucleotides, flanked by a 5' noncoding region of 56 nucleotides (including the initiation codon AUG but not the 7-methyl-guanine of the "cap structure") and by a 3' noncoding region of 95 nucleotides (including a UGA termination codon). The features of the mRNA sequence are discussed with specific attention to the selective use of particular codons, the probable existence extensively base-paired segments at the 5' terminal region and the ribosome binding site. The faithful representation of beta-globin mRNA in the PbetaG1 DNA insertion establishes the validity of used cloned DNA, initially derived from double-stranded DNA transcripts of mRNA, for studying the structure of eucaryotic genes.

Limitation of reticulocyte transfer RNA in the translation of heterologous messenger RNAs

The effect of various tRNAs on protein synthesis was investigated using a tRNA-dependent cell-free system from Ehrlich ascites cells. Ascites cell tRNA and rabbit liver tRNA were found to promote efficient translation of globin mRNA, oviduct mRNA, and encephalomycarditis (EMC) viral RNA. In contrast, reticulocyte tRNA participated efficiently only in the translation of globin mRNA; the translation of oviduct mRNA AND EMC viral RNA in the presence of reticulocyte tRNA resulted in the synthesis of relatively few large mature proteins and the accumulation of discrete, smaller polypeptides. These results suggest that isoaccepting tRNA species required for the synthesis of ovalbumin and EMC viral protein (but not hemoglobin) are probably functionally absent in reticulocyte tRNA, causing a premature, nonrandom termination of synthesis of these proteins. This provides preliminary evidence that variations in tRNA populations, frequently observed between different cell types, are large enough to define and perhaps regulate the proteins that the cell is capable of synthesizing.

Partial purification and properties of the reticulocyte guanylating enzyme

The guanylating enzyme which catalyzes the insertion of a guanine residue into one of the isoacceping tRNAHis of rabbit reticulocytes has been purified approximately one-hundred fold. It is free of nuclease activity. The enzyme does not catalyze the replacement of inserted radioactive guanine by unlabeled guanine, indicating that the reaction is irreversible. We have separated the histidyl-tRNA of reticulocytes into three isoacceptors. Previous work showed that the last histidyl-tRNA to elute from RPC-5 columns was the product of the guanylation reaction. This reports shows that the same late-eluting peak also contains the substrate for the guanylating enzyme, indicating that the guanine insertion reaction is chromatographically silent. The isoaccepting tRNAHis that is the substrate for the guanylating enzyme does not contain the hypermodified base known as Q. It is the other major reticulocyte tRNAHis that coantains Q, showing that at least in the reticulocyte the role of the guanylating enzyme is not the conversion of the Q form of tRNA to the homogeneic G form. The purified enzyme does not insert any base other than guanine into tRNA.