Kenji Ikehara's Home Page

Narasaho College

Professor of Narasaho College,
Director of Lifetime of Learning and Teaching Center
(Emeritus Professor of Nara Women's University)

(The Last Lecture of Prof. Kenji Ikehara (Feb. 22, 2008))
  at Memorial Hall of Nara Wemen's University



1. Research

(Image of the Primitive Earth)

(Picture of Electron Microscopy of Bacillus subtilis)


(How was life created on the primitive earth?)

1.1 Summary

We have proposed a new original idea on the origin of life as [GADV]-protein world hypothesis or GADV hypothesis. The idea is based on GC-NSF(a) hypothesis for creation of new original ancestor genes, GNC-SNS primitive genetic code hypothesis and protein 0th-order structure hypothesis for creation of entirely new proteins. Therefore, I consider that we could solve the riddles of the origins of life, genes, the genetic code and proteins comprehensively, based on one principle of GNC-encoding amino acids. If you have any question about our idea, please mail it to my E-mail address described below without hesitation.

E-mail address： ikehara@cc.nara-wu.ac.jp

1.1.1. Origin of Life

[GADV]-Protein World Hypothesis (GADV Hypothesis)
At present, RNA world hypothesis has been widely accepted as a trump card for solving “chicken and egg dilemma” between genes and proteins, which are observed in modern organisms. However, there exist several weak points in the hypothesis, which it might be almost impossible to solve.
In contrast, we have proposed another hypothesis, [GADV]-protein world hypothesis (abbreviated as GADV hypothesis), suggesting that life originated from [GADV]-protein world composed of various [GADV]-proteins, where [GADV] means four amino acids (Gly [G], Ala [A], Asp [D] and Val [V]), which are described in one-letter symbols.
One key point, which led to propose the hypothesis, was introduction of a new concept "pseudo-replication of [GADV]-proteins".
From standpoint of the hypothesis, it can be reasonably explained not only the way, how life originated from the protein world, but also a developmental process, upon which the "chicken and egg" relationship between genes and proteins was formed.

（References）
1.Possible Steps to the Emergence of Life: The [GADV]-Protein World Hypothesis. Kenji Ikehara, The Chemical Record, Vol. 5, Issue 2, 107-118 (2005).
2.Origins of Gene, Genetic Code, Protein and Life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis (a modified English version of the paper appeared in Viva Origino, Vol. 29, 66-85 (2001)) Kenji Ikehara, J. Biosci., Vol. 27, 165-186 (2002).

1.1.2. Origin of Genes

GC-NSF(a) Hypothesis
Two main routes for creation of new genes have been proposed. One is the gene duplication theory, which was provided by S. Ohno. The theory predicts that after duplication of a gene, one duplicate may acquire a new adaptive function, while the other duplicate retains the original function. The second is the exon shuffling theory proposed by Gilbert et al., assuming that new functional genes are created from exons shuffled among several genes.
But, two theories described above does not explain the most fundamental problems on the creation of "new original ancestor genes (NOA genes)" or entirely new genes, and, therefore, the problems how NOA genes have been created remained unsolved until now. In contrast, we have proposed new theories of the mechanism for creation of "NOA genes", from which many descendant genes could be produced, GC-NSF(a) and (GNC)n, (SNS)n primitive gene hypotheses.

（References）
1. Mechanism for Creation of “Original Ancestor Genes”. Kenji Ikehara, J. Biol. Macromol., Vol. 5, No. 2, 21-30 (2005).
2. A Possible Origin of Newly-Born Bacterial Genes: Significance of GC-rich nonstop frame on antisense strand. Kenji Ikehara, Fumiko Amada, Shigeko Yoshida, Yuji Mikata and Akira Tanaka, Nucl. Acids Res., Vol. 24, 4249-4255 (1996).
3. Unusually Biased Nucleotide Sequences on Sense Strands of Flavobacterium sp. Genes Produce Nonstop Frames on the Corresponding Antisense Strands. Kenji Ikehara, and Eriko Okazawa, Nucleic Acids Res., Vol. 21, No. 9, 2193-2199 (1993).

1.1.3. Origin of the Genetic Code

GNC-SNS Hypothesis
From analyses of microbial genes and proteins obtained from the GenomeNet Database, we found that new genes could be produced from non-stop frames on antisense sequences of microbial GC-rich genes (GC-NSF(a)).
As a next step, we performed an analysis for elucidation of the origin of the genetic codes. Consequently, we have reached a GNC-SNS primitive genetic code hypothesis, suggesting that the universal genetic code originated from the GNC code through to the SNS code, where N and S mean either of four bases (G, C, A, and T or U) and G or C, respectively.

（References）
1. A Novel Theory on the Origin of the Genetic Code: A GNC-SNS Hypothesis. Kenji Ikehara, Yoko Omori, Rieko Arai and Akiko Hirose, J. Mol. Evol., Vol. 54, 530-538 (2002).
2. Origin and Evolutionary Process of the Genetic Code. Kenji Ikehara and Yuka Niihara, Current Medicinal Chemistry (CMC) Vol. 14, No. 30, 3221-3231 (2007).

1.1.4. Origin of Proteins

Protein 0th-Order Structure Hypothesis
At the present time, it is not well known how entirely new proteins were created.
However, from our standpoints on the origins of genes and the genetic code, it can be supposed that entirely new proteins, which are not homologous with any proteins previously presented, could be created by random joining of amino acids in unique amino acid compositions, as [GADV]-amino acids encoded by GNC and SNS-encoding amino acids. We named the unique amino acid composition as protein 0th-order structure. We have previously published our original idea, protien 0th-order structure, preliminary, in several papers and reviews. Now I have also a plan to publish the idea as a new paper.

(References)
1. Origins of Gene, Genetic Code, Protein and Life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis (a modified English version of the paper appeared in Viva Origino, Vol. 29, 66-85 (2001)) Kenji Ikehara, J. Biosci., Vol. 27, 165-186 (2002).
2. Catalytic Activities of [GADV]-Peptides: Formation and establishment of [GADV]-protein world for the emergence of life. Takae Oba, Jun Fukushima, Masako Maruyama, Ryoko Iwamoto and Kenji Ikehara, Olig. Life Evol. Biosph., Vol. 35, No. 5, 447-460 (2005).

1.1.5. Further Discussion

We have proposed GADV hypothesis on the origin of life, suggesting that life originated from [GADV]-protein world through successively formed RNA-([GADV]-)protein world. Threfore, I would like to conclude that not only an independent RNA world but also a parallel protein-RNA world had never existed any time on the earth.


2. Back Ground

I studied Industrial Chemistry at Kyoto University as an undergraduate student
(Prof. Michio Kurata; Assistant Hiroyasu Utiyama and Prof. Mitsuru Takanami as Supervisors),
and received a Ph.D. in Biophysics in 1976 from Kyoto University.
From 1972-1978, I was a Member of Dept. Biophys. and Biochem. at The Univ. of Tokyo.
From 1978-1989, I worked at Dept. Chem., Fac. Sci., Nara Women's Univ., as Associate Professor.
From 1989-2008, I worked at Dept. Chem., Fac. Sci., Nara Women's Univ., as Professor.
(From 2006〜2008 Deen of Faculty of Science, Nara Women's University)
2008〜Present：Professor, Narasaho College.

2.1. The Birth Place

Moriguchi-city, Osaka, Japan, 1944

2.2. Career as a Student

Osaka Prefectural Asahi High School, 1963
Department of Industrial Chemistry, Kyoto University, 1968
Industrial Chemistry Master Course, Graduate School of Kyoto University, 1970
Industrial Chemistry Doctor Course, Graduate School of Kyoto University, 1972

2.3. Career as a Researcher

1972〜1978 Assistant, Department of Biochemistry, The University of Tokyo
1978〜1989 Associate Professor, Dept. Chem., Fac. Sci., Nara Women's Univ.
1989〜2008 Professor, Dept. Chem., Fac. Sci., Nara Women's Univ.
(2006〜2008 Deen of Faculty of Science, Nara Women's University)
2008〜Present：Professor, Narasaho College.


3. Research

3.1. Selected Books written in Japanese

1. ｢GADV仮説 −生命起源を問い直す−｣
Kyoto University Press, Kenji Ikehara (April, 2006).
Cover of the Book "GADV Hypothesis
amazon

2. 「自然学 −自然の「共生循環」を考える−」
Tokai University Press, （November, 2004）
Noboru Fujiwara, Kenji Ikehara and Yu Isobe.
Cover of the Book "Naturology"
amazon

3.2. Selected Reviews and Papers on Origin of Fundamenatal Life System

1.Origin and Evolutionary Process of the Genetic Code. Kenji Ikehara and Yuka Niihara, Current Medicinal Chemistry (CMC) Vol. 14, No. 30, 3221-3231 (2007).
2. Catalytic Activities of [GADV]-Peptides: Formation and establishment of [GADV]-protein world for the emergence of life. Takae Oba, Jun Fukushima, Masako Maruyama, Ryoko Iwamoto and Kenji Ikehara, Orig. Life Evol. Biosph., Vol. 35, No. 5, 447-460 (2005).
3. Possible Steps to the Emergence of Life: The [GADV]-Protein World Hypothesis. Kenji Ikehara, The Chemical Record, Vol. 5, Issue 2, 107-118 (2005).
4. Mechanism for Creation of “Original Ancestor Genes”. Kenji Ikehara, J. Biol. Macromol., Vol. 5, No. 2, 21-30 (2005).
5. Origins of Gene, Genetic Code, Protein and Life: comprehensive view of life systems from a GNC-SNS primitive genetic code hypothesis (a modified English version of the paper appeared in Viva Origino, Vol. 29, 66-85 (2001)) Kenji Ikehara, J. Biosci., Vol. 27, 165-186 (2002). 　
6. Simulation of Gene Evolution (evidence for GC-NSF(a) hypothesis on the origin of genes). Kenji Ikehara, Viva Origino Vol. 31, No. 3, 201-214 (2003).
7. A Novel Theory on the Origin of the Genetic Code: A GNC-SNS Hypothesis. Kenji Ikehara, Yoko Omori, Rieko Arai and Akiko Hirose, J. Mol. Evol., Vol. 54, 530-538 (2002).
8. A Possible Evolutionary Pathway of the Genetic Code deduced from the SNS Hypothesis. K. Ikehara, Viva Origino, Vol. 26, No. 4, 311-320 (1998).
9. SNS Hypothesis on the Origin of the Genetic Code. K. Ikehara, and S. Yoshida, Viva Origino, Vol. 26, No. 4, 301-310 (1998).
10. A Possible Origin of Newly-Born Bacterial Genes: Significance of GC-rich nonstop frame on antisense strand. Kenji Ikehara, Fumiko Amada, Shigeko Yoshida, Yuji Mikata and Akira Tanaka, Nucl. Acids Res., Vol. 24, 4249-4255 (1996)
11. Unusually Biased Nucleotide Sequences on Sense Strands of Flavobacterium sp. Genes Produce Nonstop Frames on the Corresponding Antisense Strands. Kenji Ikehara, and Eriko Okazawa, Nucleic Acids Res., Vol. 21, No. 9, 2193-2199 (1993)

3.3. Other Papers and Reviews

1. Ciliates uses both Variant and Universal Genetic Codes: An Evidence of Omnipotent eRF1s in the Class Litostomatea. Oanh Thi Phuong Kim, Aki Sakurai, Kazuki Saito, Koichi Ito, Kenji Ikehara and Terue Harumoto, Gene (2008) in press.
2. How is ciliate eukaryotic release factor 1 (eRF1) different from conventional eRF1s ?in vitro complementary activity of Dileptus eRF1-. Oanh T. P. Kim, Kenji Ikehara and Terue Harumoto, Jap. J. Protozool., Vol. 40, No. 1, 52-54 (2007).
3. Purification and characterization of 2-keto-D-galactonate reductase from Pseudomonas fluorescens. Ryoko Iwamoto, Ritsuko Tanimura, Kenji Ikehara and Rie Nomoto, J. Mol. Catalys. B Enzymatic Vol. 47, 43-50 (2007). Guanosine 5’-diphosphate 3’-diphosphate (ppGpp) Synthetic Activities on Escherichia coli SpoT Domains, Chizuko Fujita, Akiko Nishimura, Ryoko Iwamoto and Kenji Ikehara, Biosci. Biotech. Biochem. Vol. 66, No. 7, 1515-1523 (2002).
4. Identification of an Indispensable Amino Acid for ppGpp Synthesis of Escherichia coli SpoT protein, Chizuko Fujita, Maki Maeda, Takako Fujii, Ryoko Iwamoto and Kenji Ikehara, Biosci. Biotech. Biochem. Vol. 66, No. 12, 2735-2738 (2002).
5. Guanylate Kinase of Escherichia coli K-12. Daniel Gentry, Chikh Bengra, Kenji Ikehara, and Michael Cashel, J. Biol. Chem., Vol. 268, No. 19, 14316-14321 (1993)
6. Residual Guanosine 3', 5'-Bispyrophosphate Synthetic Activity of relA Null Mutants can be Eliminated by spoT Null Mutations. Hua Xiao, Miklos Kalman, Kenji Ikehara, Sharon Zemel, Gad Glaser, and Michael Cashel, J. Biol. Chem., Vol. 266, No. 9, 5980-5990 (1991)
7.　Characterization of the spoT Gene of Escherichia coli. Edoardo Sarubbi, Kenneth E. Rudd, Hua Xiao, Kenji Ikehara, Miklos Kalman, and Michael Cashel J. Biol. Chem., Vol. 264, No. 25, 15074-15082 (1989)
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