RNA CODEWORDS AND PROTEIN SYNTHESIS. II. NUCLEOTIDE SEQUENCE OF A VALINE RNA CODEWORD

A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell

The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.

Looking Back: A Short History of the Discovery of Enzymes and How They Became Powerful Chemical Tools

Enzymatic approaches to challenges in chemical synthesis are increasingly popular and very attractive to industry given their green nature and high efficiency compared to traditional methods. In this historical review we highlight the developments across several fields that were necessary to create the modern field of biocatalysis, with enzyme engineering and directed evolution at its core. We exemplify the modular, incremental, and highly unpredictable nature of scientific discovery, driven by curiosity, and showcase the resulting examples of cutting-edge enzymatic applications in industry.

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.

A new oxygen modification cyclooctaoxygen binds to nucleic acids as sodium crown complex

BACKGROUND

Oxygen exists in two gaseous and six solid allotropic modifications. An additional allotropic modification of oxygen, the cyclooctaoxygen, was predicted to exist in 1990.

METHODS

Cyclooctaoxygen sodium was synthesized in vitro from atmospheric oxygen, or catalase effect-generated oxygen, under catalysis of cytosine nucleosides and either ninhydrin or eukaryotic low-molecular weight RNA. Thin-layer chromatographic mobility shift assays were applied on specific nucleic acids and the cyclooctaoxygen sodium complex.

RESULTS

We report the first synthesis and characterization of cyclooctaoxygen as its sodium crown complex, isolated in the form of three cytosine nucleoside hydrochloride complexes. The cationic cyclooctaoxygen sodium complex is shown to bind to nucleic acids (RNA and DNA), to associate with single-stranded DNA and spermine phosphate, and to be essentially non-toxic to cultured mammalian cells at 0.1-1.0mM concentration.

CONCLUSIONS

We postulate that cyclooctaoxygen is formed in most eukaryotic cells in vivo from dihydrogen peroxide in a catalase reaction catalyzed by cytidine and RNA. A molecular biological model is deduced for a first epigenetic shell of eukaryotic in vivo DNA. This model incorporates an epigenetic explanation for the interactions of the essential micronutrient selenium (as selenite) with eukaryotic in vivo DNA.

GENERAL SIGNIFICANCE

Since the sperminium phosphate/cyclooctaoxygen sodium complex is calculated to cover the active regions (2.6%) of bovine lymphocyte interphase genome, and 12.4% of murine enterocyte mitotic chromatin, we propose that the sperminium phosphate/cyclooctaoxygen sodium complex coverage of nucleic acids is essential to eukaryotic gene regulation and promoted proto-eukaryotic evolution.

Memories of a senior scientist: on passing the fiftieth anniversary of the beginning of deciphering the genetic code

2011 marked the fiftieth anniversary of breaking the genetic code in 1961. Marshall Nirenberg, the National Institutes of Health (NIH) scientist who was awarded the Nobel Prize in Physiology or Medicine in 1968 for his role in deciphering the code, wrote in 2004 a personal account of his research. The race for the code was a competition between the NIH group and Severo Ochoa's laboratory at New York University (NYU) School of Medicine, where I was a graduate student and conducted many of the experiments. I am now 83 years old. These facts prompt me to recall how I, together with Joe Speyer, an instructor in the Department of Biochemistry at NYU, unexpectedly became involved in deciphering the code, which also became the basis of my PhD thesis. Ochoa won the Nobel Prize in Physiology or Medicine in 1959 for discovering polynucleotide phosphorylase (PNP), the first enzyme found to synthesize RNA in the test tube. The story of how PNP made the deciphering of the code feasible is recalled here.

Dual functions of codons in the genetic code

The discovery of the genetic code provided one of the basic foundations of modern molecular biology. Most organisms use the same genetic language, but there are also well-documented variations representing codon reassignments within specific groups of organisms (such as ciliates and yeast) or organelles (such as plastids and mitochondria). In addition, duality in codon function is known in the use of AUG in translation initiation and methionine insertion into internal protein positions as well as in the case of selenocysteine and pyrrolysine insertion (encoded by UGA and UAG, respectively) in competition with translation termination. Ambiguous meaning of CUG in coding for serine and leucine is also known. However, a recent study revealed that codons in any position within the open reading frame can serve a dual function and that a change in codon meaning can be achieved by availability of a specific type of RNA stem-loop structure in the 3'-untranslated region. Thus, duality of codon function is a more widely used feature of the genetic code than previously known, and this observation raises the possibility that additional recoding events and additional novel features have evolved in the genetic code.

Discovery of proteomic code with mRNA assisted protein folding

The 3x redundancy of the Genetic Code is usually explained as a necessity to increase the mutation-resistance of the genetic information. However recent bioinformatical observations indicate that the redundant Genetic Code contains more biological information than previously known and which is additional to the 64/20 definition of amino acids. It might define the physico-chemical and structural properties of amino acids, the codon boundaries, the amino acid co-locations (interactions) in the coded proteins and the free folding energy of mRNAs. This additional information, which seems to be necessary to determine the 3D structure of coding nucleic acids as well as the coded proteins, is known as the Proteomic Code and mRNA Assisted Protein Folding.

Decoding the genome: a modified view

Transfer RNA's role in decoding the genome is critical to the accuracy and efficiency of protein synthesis. Though modified nucleosides were identified in RNA 50 years ago, only recently has their importance to tRNA's ability to decode cognate and wobble codons become apparent. RNA modifications are ubiquitous. To date, some 100 different posttranslational modifications have been identified. Modifications of tRNA are the most extensively investigated; however, many other RNAs have modified nucleosides. The modifications that occur at the first, or wobble position, of tRNA's anticodon and those 3'-adjacent to the anticodon are of particular interest. The tRNAs most affected by individual and combinations of modifications respond to codons in mixed codon boxes where distinction of the third codon base is important for discriminating between the correct cognate or wobble codons and the incorrect near-cognate codons (e.g. AAA/G for lysine versus AAU/C asparagine). In contrast, other modifications expand wobble codon recognition, such as U*U base pairing, for tRNAs that respond to multiple codons of a 4-fold degenerate codon box (e.g. GUU/A/C/G for valine). Whether restricting codon recognition, expanding wobble, enabling translocation, or maintaining the messenger RNA, reading frame modifications appear to reduce anticodon loop dynamics to that accepted by the ribosome. Therefore, we suggest that anticodon stem and loop domain nucleoside modifications allow a limited number of tRNAs to accurately and efficiently decode the 61 amino acid codons by selectively restricting some anticodon-codon interactions and expanding others.

THE SEQUENTIAL SYNTHESIS OF THE POLYPEPTIDE CHAIN OF SERUM ALBUMIN BY THE MICROSOME FRACTION OF RAT LIVER

1. The isolated microsome fraction of regenerating rat liver was incubated with cell sap, a source of energy and [(35)S]methionine, [(14)C]isoleucine or [(14)C]leucine for different periods of time, and microsomal albumin isolated. 2. The distribution of these isotopes in albumin was determined by separation of tryptic peptides from the protein. Radioactivity was measured in peptides either qualitatively by radioautography or quantitatively by labelling with both (3)H and (14)C. 3. A gradient of radioactivity existed at all times in albumin isolated after incubating microsomes. 4. The shorter the incubation time the fewer the peptides labelled in albumin, but the peptides with highest specific activity after short incubation times corresponded to those with highest specific activities after long incubation times. 5. Leucine released from the C-terminus of albumin had a higher specific activity than the mean specific activity of the remaining leucine residues in albumin. 6. The peptide with the highest specific activity in albumin is probably derived from the C-terminus of the protein. 7. [(14)C]Glutamic acid is incorporated into the N-terminus of albumin after incubating the microsome fraction with this isotopically labelled amino acid, cell sap and a source of energy. The specific activity of the N-terminal glutamic acid under these conditions is less than the mean specific activity of the remaining glutamic acid and glutamine residues in albumin. 8. The results are interpreted as reflecting a sequential synthesis of serum albumin in the isolated microsome fraction of rat liver. The direction of synthesis of albumin is from the N-terminus towards the C-terminus. 9. The bulk of incorporation of radioactive amino acid into albumin in the isolated microsome fraction is due to completion of partially completed, pre-existing peptide and polypeptide chains. A limited synthesis of new chains of albumin does, however, occur.

Biochemical assay designed to detect formation of recombination intermediates in vitro

A biochemical assay that is designed to detect recombination intermediates formed in vitro is described. The assay measures the fusion of two essentially homologous plasmids, one of which is radioactively labeled and the other of which carries several copies of the lac operator. The fusion product is radioactive and can be bound to a nitrocellulose filter by lac repressor. This assay for genome fusion is rapid and readily applicable to the many fractions that result during enzyme purification. The fused product is not destroyed in the assay and may be recovered from the filter for further analysis by electron microscopy. The product is then seen to consist of figure 8 structures that can be cleaved by the restriction enzyme EcoRI to give chi forms, structures similar to those recovered from recombination-proficient cells. It is expected that this assay will be useful in the purification of the "recombinase-type" activity detected in crude cell lysates. To demonstrate this point, the assay was applied to the protein fractions recovered from a molecular sieve column. The results indicate that the fusion activity has an apparent molecular weight of 50,000--100,000.

The chain growth rate of T4 lysozyme in vitro

The average interval between attachment of a 30S ribosomal subunit to bacteriophage T4 lysozyme mRNA and the completion of synthesis of lysozyme protein has been measured in vitro. The measured completion times yield rates of polypeptide chain propagation of 1.6 and 3.0 amino acids per second at 25 degrees C and 31 degrees C, respectively.

Demonstration of the universality of the genetic code in vivo by comparison of the coat proteins synthesized in different plants by tobacco mosaic virus RNA

The amino acid sequence of the coat protein of tobacco mosaic virus (TMV) synthesized in the garden zinnia (Compositae family) is compared with that synthesized in tobacco (Solanaceae family) by using the same preparation of TMV-RNA as messenger. The Compositae family is the most advanced group, and the Solanaceae family is a relatively advanced group in the plant kingdom. Both amino acid sequences are identical, including acetylserine as the N-terminal amino acid. This gives direct evidence that the RNA codon in vivo in the plant kingdom is universal between Compositae and Solanaceae families.

Fine structure of RNA codewords recognized by bacterial, amphibian, and mammalian transfer RNA

Nucleotide sequences of 50 RNA codons recognized by amphibian and mammalian liver transfer RNA preparations were determined and compared with those recognized by Escherichia coli transfer RNA. Almost identical translations were obtained with transfer RNA from guinea pig liver, Xenopus laevis liver (South African clawed toad), and E. coli. However, guinea pig and Xenopus transfer RNA differ markedly from E. coli transfer RNA in relative response to certain trinucleotides. Transfer RNA from mammalian liver, amphibian liver, and amphibian muscle respond similarly to trinucleotide codons. Thus the genetic code is essentially universal, but transfer RNA from one organism may differ from that of another in relative response to some codons.

RNA CODEWORDS AND PROTEIN SYNTHESIS. THE EFFECT OF TRINUCLEOTIDES UPON THE BINDING OF SRNA TO RIBOSOMES

A rapid, sensitive method is described for measuring C(14)-aminoacyl-sRNA interactions with ribosomes which are specifically induced by the appropriate RNA codewords prior to peptide-bond formation. Properties of the codeword recognition process and the minimum oligonucleotide chain length required to induce such interactions are presented. The trinucleotides, pUpUpU, pApApA, and pCpCpC, but not dinucleotides, specifically direct the binding to ribosomes of phenylalanine-, lysine-, and proline-sRNA, respectively. Since 5'-terminal, 3'-terminal, and internal codewords differ in chemical structure, three corresponding classes of codewords are proposed. The recognition of each class in this system is described. The template efficiency of trinucleotide codewords is modified greatly by terminal phosphate. Triplets with 5'-terminal phosphate are more active as templates than triplets without terminal phosphate. Triplets with 3'- or 3' (2')-terminal phosphate are markedly less active as templates. These findings are discussed in relation to the probable functions of terminal codewords. The modification of RNA and DNA codewords, converting sense into missense or nonsense codewords, is suggested as a possible regulatory mechanism in protein synthesis.