Kenji Ikehara

A novel theory on the origin of the genetic code: a GNC-SNS hypothesis.

Abstract. We have previously proposed an SNS hypothesis on the origin of the genetic code (Ikehara and Yoshida 1998). The hypothesis predicts that the universal genetic code originated from the SNS code composed of 16 codons and 10 amino acids (S and N mean G or C and either of four bases, respectively). But, it must have been very difficult to create the SNS code at one stroke in the beginning. Therefore, we searched for a simpler code than the SNS code, which could still encode water-soluble globular proteins with appropriate three-dimensional structures at a high probability using four conditions for globular protein formation (hydropathy, α-helix, β-sheet, and β-turn formations). Four amino acids (Gly [G], Ala [A], Asp [D], and Val [V]) encoded by the GNC code satisfied the four structural conditions well, but other codes in rows and columns in the universal genetic code table do not, except for the GNG code, a slightly modified form of the GNC code. Three three-amino acid systems ([D], Leu and Tyr; [D], Tyr and Met; Glu, Pro and Ile) also satisfied the above four conditions. But, some amino acids in the three systems are far more complex than those encoded by the GNC code. In addition, the amino acids in the three-amino acid systems are scattered in the universal genetic code table. Thus, we concluded that the universal genetic code originated not from a three-amino acid system but from a four-amino acid system, the GNC code encoding [GADV]-proteins, as the most primitive genetic code.

Origins of gene, genetic code, protein and life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis.

We have investigated the origin of genes, the genetic code, proteins and life using six indices (hydropathy, α-helix, β-sheet and β-turn formabilities, acidic amino acid content and basic amino acid content) necessary for appropriate three-dimensional structure formation of globular proteins. From the analysis of microbial genes, we have concluded that newly-born genes are products of nonstop frames (NSF) on antisense strands of microbial GC-rich genes [GC-NSF(a)] and from SNS repeating sequences [(SNS)n] similar to the GC-NSF(a) (S and N mean G or C and either of four bases, respectively). We have also proposed that the universal genetic code used by most organisms on the earth presently could be derived from a GNC-SNS primitive genetic code. We have further presented the [GADV]-protein world hypothesis of the origin of life as well as a hypothesis of protein production, suggesting that proteins were originally produced by random peptide formation of amino acids restricted in specific amino acid compositions termed as GNC-, SNS and GC-NSF(a)-0th order structures of proteins. The [GADV]-protein world hypothesis is primarily derived from the GNC-primitive genetic code hypothesis. It is also expected that basic properties of extant genes and proteins could be revealed by considerations based on the scenario with four stages

Catalytic activities of [GADV]-peptides : Formation and establishment of [GADV]-protein world for the emergence of life

We have previously postulated a novel hypothesis for the origin of life, assuming that life on the earth originated from “[GADV]-protein world”, not from the “RNA world” (see Ikeharas review, 2002). The [GADV]-protein world is constituted from peptides and proteins with random sequences of four amino acids (glycine [G], alanine [A], aspartic acid [D] and valine [V]), which accumulated by pseudo-replication of the [GADV]-proteins. To obtain evidence for the hypothesis, we produced [GADV]-peptides by repeated heat-drying of the amino acids for 30 cycles ([GADV]-P30) and examined whether the peptides have some catalytic activities or not. From the results, it was found that the [GADV]-P30 can hydrolyze several kinds of chemical bonds in molecules, such as umbelliferyl-β-D-galactoside, glycine-p-nitroanilide and bovine serum albumin. This suggests that [GADV]-P30 could play an important role in the accumulation of [GADV]-proteins through pseudo-replication, leading to the emergence of life. We further show that [GADV]-octapaptides with random sequences, but containing no cyclic compounds as diketepiperazines, have catalytic activity, hydrolyzing peptide bonds in a natural protein, bovine serum albumin. The catalytic activity of the octapeptides was much higher than the [GADV]-P30 produced through repeated heat-drying treatments. These results also support the [GADV]-protein-world hypothesis of the origin of life (see Ikeharas review, 2002). Possible steps for the emergence of life on the primitive earth are presented.

Pseudo-Replication of [GADV]-Proteins and Origin of Life

The RNA world hypothesis on the origin of life is generally considered as the key to solve the “chicken and egg dilemma” concerning the evolution of genes and proteins as observed in the modern organisms. This hypothesis, however, contains several serious weak points. We have a counterproposal called [GADV]-protein world hypothesis, abbreviated as GADV hypothesis, in which we have suggested that life originated from a [GADV]-protein world, which comprised proteins composed of four amino acids: Gly [G], Ala [A], Asp [D], and Val [V]. A new concept “pseudo-replication” is crucial for the description of the emergence of life. The new hypothesis not only plausibly explains how life originated from the initial chaotic protein world, but also how genes, genetic code, and proteins co-evolved.

Synthesis and evaluation of nitro 5-deazaflavins as novel bioreductive antitumor agents

Abstract A series of nitro 5-deazaflavins, 5-deazaflavins possessing a nitro group at C(6)–C(9) position, has been designed and synthesized as a novel class of bioreductive nitrohetero-aromatic compounds and their cytotoxicities towards L1210 and KB cells were evaluated. It has been found that the nitro 5-deazaflavins undergo one electron reduction on the nitro group and undergo two electrons or “(net) hydride” reduction on the C(5)-C(4a)-C(10a)-N(1) redox system. They showed much more potent antitumor activities than the other 5-deazaflavins bearing no nitro group. These results suggest that an activation of nitro group by biological one electron reduction is crucial for an expression of cytotoxicity.

Evaluation of differential hypoxic cytotoxicity and electrochemical studies of nitro 5-deazaflavins

Abstract Cytotoxicities of nitro 5-deazaflavins were evaluated in vitro towards hypoxic and oxic Chinese hamster cells (V79). 6-Nitro and 8-nitro derivatives were generally more toxic towards hypoxic cells than oxic cells, showing marked hypoxic selectivity. In contrast, 7-nitro and 9-nitro derivatives showed no significant hypoxic selectivity. Electrochemical study using cyclic voltammetry (CV) revealed that 6-nitro and 8-nitro derivatives generate a stable two electrons reduction product as well as a stable one electron reduction product and that 7-nitro and 9-nitro derivatives afford an unstable one electron reduction product. These results strongly support that not solely electron affinity but also stability of the one electron reduction products is crucial for the differential hypoxic cytotoxicities of nitro 5-deazaflavins.

Enzymatic synthesis of 2-keto-d-gluconate and 2-keto-d-galactonate from d-glucose and d-galactose with cell culture of Pseudomonas fluorescens and 2-keto-galactonate from d-galactono 1,4-lactone with partially purified 2-ketogalactonate reductase

Abstract 2-Keto- d -gluconate and 2-keto- d -galactonate were prepared from d -glucose (with a yield of 40%) and d -galactose (with a yield of 25%), respectively, with cell culture of Pseudomonas fluorescens . However, 2-keto- d -mannoate was not prepared in this method. The time courses of the reactions showed that 2-keto- d -gluconic acid and 2-keto- d -galactonic acid were produced from d -glucose and d -galactose through d -gluconate and d -galactonate, respectively. When using d -galactono 1,4-lactone as a starting material, 2-keto- d -galactonate was produced with partially purified NADP-dependent 2-ketogalactonate reductase from P. fluorescens . Some fundamental properties of the 2-ketogalactonate reductase were compared with those of 2-ketogluconate reductase from Acetobacter and Gluconobacter .

Evolutionary Steps in the Emergence of Life Deduced from the Bottom-Up Approach and GADV Hypothesis (Top-Down Approach).

It is no doubt quite difficult to solve the riddle of the origin of life. So, firstly, I would like to point out the kinds of obstacles there are in solving this riddle and how we should tackle these difficult problems, reviewing the studies that have been conducted so far. After that, I will propose that the consecutive evolutionary steps in a timeline can be rationally deduced by using a common event as a juncture, which is obtained by two counter-directional approaches: one is the bottom-up approach through which many researchers have studied the origin of life, and the other is the top-down approach, through which I established the [GADV]-protein world hypothesis or GADV hypothesis on the origin of life starting from a study on the formation of entirely new genes in extant microorganisms. Last, I will describe the probable evolutionary process from the formation of Earth to the emergence of life, which was deduced by using a common event—the establishment of the first genetic code encoding [GADV]-amino acids—as a juncture for the results obtained from the two approaches.

[GADV]-Protein World Hypothesis on the Origin of Life

RNA world hypothesis is widely accepted still now, as an idea by which the origin of life might be explained. But, there are many weak points in the hypothesis. In contrast, I have proposed a more reasonable [GADV]-protein world hypothesis or GADV hypothesis, suggesting that life originated from the protein world, which was formed by pseudo-replication of [GADV]-proteins. In this communication, I will discuss about the origin of life from the point of view of the GADV hypothesis.

Ciliates use both variant and universal genetic codes: evidence of omnipotent eRF1s in the class Litostomatea.

Stop codon reassignments have occurred very frequently in ciliates. In some ciliate species, the universal stop codons UAA and UAG are translated into glutamine, while in some other species, the universal stop codon UGA appears to be translated into cysteine or tryptophan. The class Litostomatea has been hypothesized to be the only group of ciliates using the universal genetic code. However, the hypothesis was based on a statistical analysis of quite small sequence dataset which was insufficient to elucidate the codon usage of the class among such highly deviated phylum. In this study, together with the updated database sequence analysis for the class, we approached the problem of stop codon usage by examining the capacity of the translation termination factor eRF1 for recognizing stop codons. Using in vivo assay systems in budding yeast, we estimated the activity of eRF1 from two litostome species Didinium nasutum and Dileptus margaritifer. The results clearly showed that Didinium and Dileptus eRF1s efficiently recognize all three stop codons. This is the first experimental evidence that strongly supports the hypothesis that litostome ciliates use universal genetic code.