J. Biol. Macromol., 5(2), 21-30 (2005)

Review

Mechanisms for Creation of “Original Ancestor Genes”
Kenji Ikehara
Department of Chemistry, Faculty of Science, Nara Women’s University
Kita-uoya-nishi-machi, Nara, Nara 630-8506, Japan
Received June 24, 2005; Accepted June 29, 2005

Two main theories on creation of new
genes
Diversity of organisms on the earth

shuffled among several genes (Fig. 1B).
On the other hand, proteins are generallyclassified

asprotein

and

to

the

would be tightly coupled to the evolution ofsuperfamilies,

new gene functions.

sequence-structure information and catalytic

Two main routes foraccordingfamilies

creation of new genes have been proposed

properties.

(Fig. 1).

One is the gene duplication theory,

protein family is composed of proteins withwhich was provided by S. Ohno (1970) (1).

similar amino acid sequences and similar

The theory predicts that after duplication of afunctions, which originated from one original

gene, one duplicate may acquire a newgene, whereas a protein superfamily contains

adaptive function, while the other duplicate

several protein families with similar amino

retains the original function (Fig. 1A).

acid sequences but with different catalyticThesecond is the exon shuffling theory proposed

As can be seen in Fig. 2, afunctions.

by Gilbert et al. (1997) (2), assuming that

Therefore, not only proteins belonging to

new functional genes are created from exonsa protein family but also those in a(A)an original genea new gene(B)an original genean original gene(exon shuffling)a new geneFig. 1. Two theories proposed for creation of new genes. (A) Geneduplication theory (1). (B) Exon shuffling theory (2).

22

Original ancestor genes

encoding proteins which acquired newfunction to form a protein family and“original ancestor gene” indicates the firstancestor gene encoding the first protein
among a protein superfamily (Fig. 2).
This means that two theories describedabove does not explain the most fundamental
problems on the creation of “originalancestor genes” and that the problems areremained unsolved until now.

So, in thisreview the mechanism for creation of“original ancestor genes”, from which many
descendant genes could be produced, isdiscussed
Fig. 2.
Individual proteins(small black dots) should be
produced from “original ancestor
genes” (open circles) and from“original genes” (grey circles).
Large ellipsoids small ellipsoids
indicate protein superfamilies andprotein families, respectively.

from

a

standpoint

of

our

GC-NSF(a) and (GNC)n, (SNS)n primitive
gene hypotheses (3, 4).

GC-NSF(a) Hypothesis for Creation of“Original Ancestor” Genes under the
Universal Genetic CodeWe have proposed one hypothesis on the

superfamily originated from one common
original ancestor protein.

This indicates thatall proteins in the family and the superfamily
were produced by expression of genes
created by gene duplications (Fig. 2).
theory and exon shuffling theory, areessential molecular mechanisms for creationof new genes, both routes require preexisting,
Therefore, both of the twotheories do not explain the way how to create
original ancestor genes, which are quite
different from preexisting genes, since newgenes are produced by modification fromsense sequences of the parental genes.

performing researches based on the following
considerations (3).

If new genes werecreated on the earth at present, from whatkind of DNA sequences could “original

Although two theories, gene duplication

original genes.

origin of genes about 10 years ago, while

Here,“original gene” means a parental geneancestor genes” have been created under theuniversal

genetic

code?

Analysesof

microbial genes and proteins obtained fromthe GenomeNet Database, led us the idea thatnew “original ancestor genes” could be
produced from non-stop frames on antisensesequencesofmicrobial

GC-richgenes(GC-NSF(a)), as described below (Fig. 3) (3).
The GC contents of microbial genes are
distributed over an extremely wide range,from about 25 to 75%.

Compositions of

K. Ikehara

23

about half the number of amino acids infrom seven genomes of bacteria and archaea.

proteins largely change as the GC contents ofThis means that when we judge whether or

the genes increased or decreased under GC-

not polypeptide chains can be folded intoor AT-mutation pressure (4, 5).

water-soluble globular structures required for

It isexpected that the fundamental properties of

enzymatic

globular proteins, which are given by six

indexes are utilized as necessary conditions.

α-helix,

Thus, we first searched for the nucleotide

β-sheet, β-turn formabilities, acidic, andsequences by using the indexes where new

basic amino acid contents), are invariable“original ancestor genes” could be createdagainst the differences of GC contents among

under the universal genetic code.

genes followed by those of amino acidpurpose, we investigated the six structuralcompositions.

indexes of hypothetical proteins encoded bystructuralindexes(hydropathy,

The reason for this isfunctions,

the

six

structural

For this

intopossible five reading frames of extant

appropriate three-dimensional structures evenbacterial and archaeal genes, which weinobtained from a gene bank.

becauseproteins

every

must

microbialbecellfoldedcarrying

a

we

found

that

From thechromosomal DNA with different GC content.

results,

The structural indexes of whole proteins,polypeptide chains encoded by antisense

which determine the secondary and tertiary

sequences on genes with high GC contents

structures of proteins, were calculated by(more than 60%) could be folded into

multiplying amino acid composition with theglobular structures in water or cells at a highindexes of 20 amino acids from Stryer’s

probability.

textbook (6).

(pNSF) at which no stop codon appears in a

Moreover,hypotheticaltheprobability

The analyses of the six indexes ofreading frame increases abruptly beyond at

microbial proteins revealed that all indexes

about 60% GC content, which is caused byare expectedly almost constant against theunusually biased base compositions at threevariation of GC content of genes obtainedcodon position (7).

P

a GC-rich gene (an original gene)T

Duplication
Pa GC-rich geneTP

a GC-rich geneTta GC-NSF(a)pMaturation from a NSF(a) to a New GC-rich GeneTa new GC-rich "original ancestor gene"Fig. 3. GC-NSF(a) primitive gene hypothesis for creation of “original ancestor genes”
under the universal genetic code.
The hypothesis predicts that new “original ancestor
genes” originate from nonstop frames on antisense strands of GC-rich genes(GC-NSF(a)s).

P

24

Original ancestor genes

It was also found that proteins encoded

From the results, it was found that theby GC-NSF(a) hypothetical genes havecomputer-generated SNS code satisfies thefavorable properties in that they are able tosix conditions when the contents of G and C

adapt to novel substrates since the proteinsat the first codon position were at aroundwould have some flexibility owing to slightly

55% and 45%, respectively, and when every

highersmallerfour base was contained at a ratio of abouthydrophobicity indexes of the proteins than

one-forth at the second codon position.

those of actual proteins.

Thus, we would

Base compositions at the third position could

like to assert here that the GC-NSF(a)s easily

not be restricted to a narrow range due to thefound on GC-rich microbial genomes mustdegeneracy of the genetic code at thatbe the field, from which new “original

position.

ancestor genes” could be produced on thethere was a high probability that polypeptide

earth at present (Fig. 3) (3, 8).

chains composed of SNS-encoding amino

glycinecontents

andHowever, this also means thatacids ([L], [P], [H], [Q], [R], [V], [A], [D],Hypothesis on the Origin of the
Genetic Code
When several months passed after the[E], and [G]) should be folded into globular
GNC primeval genetic code

proposition of the GC-NSF(a) primitive gene
hypothesis, I noticed that base compositions

U
G

C

A

G

Val Ala Asp Gly C

of the GC-NSF(a)s can be approximated at
the three codon positions as SNS or[(G/C)N(C/G)] at a limit to the GC-rich side(4, 5, 9).

SNS primitive genetic code

To confirm that the SNS code has

U

C

A

G

a powerful ability coding for water-soluble

C Leu Pro

His Arg C

globular proteins, SNS compositions in three

C Leu Pro

Gln Arg G

codon positions were generated by usingG

Val Ala Asp Gly C

computer-generated random numbers.

G

Val Ala Glu

S

Gly G

and N mean either of G or C, and either offour bases, A, U (T), G and C, respectively.
We then selected SNS compositions that
could satisfy the six structural conditions
obtainedfromextantproteins.

The

structural indexes of a hypothetical protein
were similarly calculated with amino acidcomposition

and

the

indexesofthecorresponding amino acids as describedabove.

The Universal Genetic CodeFig. 4. GNC-SNS primitive genetic
code hypothesis, which we havepresented to explain the evolutionary
pathway to the universal genetic code(5). The hypothesis postulates that theuniversal genetic code originated fromthe GNC primeval genetic code throughthe SNS primitive code.

K. Ikehara

structures.

Thus, we have provided an SNS

25

coding ability.

From the analyses anddiscussion on the origin of the genetic code,

primitive genetic code hypothesis (9).
In addition, we confirmed that secondary
structures and hydropathy profiles of proteins

we have proposed the GNC-SNS primitive
genetic code hypothesis (Fig. 4) (5).

encoded by (SNS)n hypothetical genes, which

Under the GNC and SNS genetic codes,

were generated by a computer, gave mixed

group coding for the production of functional

profilesofstructuresproteins should be adopted to avoid meeting(α-helix,

β-sheet,andofstop codons, otherwise non-assigned tripletshydrophobic and hydrophilic regions similaror the resulting stop codons would often

to those of existing proteins (data not shown).

appear in the random sequences at extremely

threesecondaryandβ-turn)Furthermore, we investigated what kindhigh frequencies.

At present, however, it isof genetic code that is much simpler thanunknown about what makes it possible to

SNS primitive genetic code could encode

enable group coding.

water-soluble globular proteins.

For this

purpose, four conditions (hydropathy, α-helix,
β-sheet, and β-turn formations) out of the six

Establishment of the GNC primeval
genetic code

conditions were used to determine which

Shimizu (11) has reported that RNAs bearing

genetic code could encode water-soluble

anticodon nucleotides at the 5' ends and a

globular proteins.

Consequently, it was

discriminator base at the 3' ends named as

found that GNC would be used as the mostC4N could accept the cognate amino acid byprimeval genetic code on the primitive earth,

the lock-and-key relationship, and that the

because four [GADV]-amino acids encoded

C4N

by the code well satisfied the four structural

specifically with their cognate amino acids.

conditions.

This conclusion is the same as

From theoretical analysis of conformation of

the antiquity of the "GNC" code, which was

the hydrogen-bonded C4N complexes, it isfirst proposed by Eigen and Schuster (10)shown that some conformational changes arefrom an independent standpoint of the protein

induced

[G]

[V]

[G]

[G]

GCC

GAC

GCC

GGC

CGG

CUG

CGG

CGG

[A]

[D]

[A]

[A]

complexes

in

the

were

aminoacylated

anticodon

trinucleoside

Amino acid-oligonucleotide

Fig. 5.
Establishment of GNC primeval genetic code by specificstereo-chemicalbindingof[GADV]-amino
acids
with
GNC-containing oligonucleotides.
GNC codons arranged
randomly but sequentially were used as imitations of genes before
creation of the most primitive “original ancestor gene”(single-stranded (GNC)n gene).

26

Original ancestor genes

diphosphatebydiscriminatorthebinding

base.

of

the

Conformationalcode.

It is also supposed that [GADV]-

proteins synthesized under the GNC primevalchanges of C4N and the amino acid are also

genetic

induced by the binding of the amino acid to[GADV]-amino acids, since the code can

C4N (12).

translate GNC codons into the four aminoSo, it is assumed that [GADV]-proteinscode

acids.

must

contain

only

The reason why random peptide

accumulated by pseudoreplication of thebond formation among [GADV]-amino acids

proteins

world

made it possible to produce water-soluble

synthesized nucleotides and oligonucleotides

globular proteins is that the composition(4, 8), and that oligonucleotides containing

composed of [GADV]-amino acids is one of

GNC were aminoacylated with cognate

the 0th-order structures of proteins (4).

in

[GADV]-protein[GADV]-amino acid and confronted with
one is tRNA (anticodon) and the other is

Deduced Pathway for Creation of“Original Ancestor (GNC)n Genes”

mRNA (codon) (Fig. 5).

The random

As described above, we have proposed that

lengthwise arrangement of the complexes

the first genetic code appeared on the earth

should accelerate [GADV]-protein synthesismust be the GNC primeval genetic code.

at a higher rate than the synthesis ofThis implies that even randomly GNC[GADV]-proteins under the absence of therepeating sequences could be utilized as a

C4N-likekindcomplementary complexes similarly as thatcomplexes,

leadingtoestablishment of the GNC primeval geneticofwater-soluble

functional

genes

encoding

globularproteins

onthe(One Original (GNC)n Gene)5'-ggcgccgtcgtcgtcggcgacgccgcc
3'-ccgcggcagcagcagccgctgcggcgg

Original
genetic function

route 1

gtcggcgtcggcgtcgacggcgtcggcggcgac-3'
cagccgcagccgcagctgccgcagccgccgctg-5'(Gene Duplication)route 2

Original
genetic function(Accumulation of Mutation)(a modified gene from sense sequence)(a new original gene from antisense sequence)

Fig. 6.
Two routes for producing new genes. Once one original (GNC)n gene
was produced, new genes were easily produced by using the original genethrough two routes, one is from sense sequence and the other is from antisensesequence of the original gene.
From route 1, new gene could be produced asa modified gene of the original gene, and from route 2, new gene could becreated as an “original ancestor gene”.

K. Ikehara

primitive earth.

To exhibit genetic functions

27of proteins existed before.

These suggest

more effectively, GNC codons must bethat antisense sequences of primeval genes,

combined by covalent bonds, resulting in(GNC)n, would be favorable for synthesis offormation

new “original ancestor [GADV]-proteins”

of

the

most

primitive

single-stranded RNA genes corresponding tounder the most primitive GNC code.

modern mRNA, after a lapse of some timethe [GADV]-proteins must lead to create thefrom the establishment of the GNC primeval

GNC primeval genetic code followed bygenetic(GNC)ncode.

Lately,double-stranded

primeval

genes,

Thus,

resultedin(GNC)n genes were formed by binding GNC

formation of the most primitive fundamental

codons with covalent bonds as the case oflife system.

formation of the single-stranded (GNC)n
from

the

Deduced Pathway for Creation of“Original Ancestor (SNS)n Genes”

sequenceswere

As seen in Fig. 7, it is considered that gene,symmetric between codons on sense andgenetic code and protein were coevolved andantisense sequences.

must be coevolved in the period from thegenes as described above.
(GNC)ngenes

single-stranded

Double-stranded

evolved
GNC

This enabled for both sequences to use
for production of new genes.

Namely, twoestablishment of the fundamental life system
to the present time, since three objects areroutes for creation new genes are consideredintimately related to each other.

(Fig. 6).

reasons are as follows.

One route is for producing new

The

Proteins can not be

genes encoding modified and similar proteins

reproduced without both genes and genetic

to the original proteins. The other is a route

code,

producing new “original ancestor genes”

fundamental life system.

encoding new proteins with quite different

on genes can not be expressed without bothamino acid sequences from every sequence

proteineous enzymes and genetic code.

after

the

establishment(RNA, DNA)the

Genetic functions

Protein

Gene

of

Genetic code

(Oligonucleotides)

Fig. 7. Coevolution among gene, genetic code and protein. Threeobjects composed of gene, genetic code and protein have coevolved,
after establishment of the most fundamental life system, since they are
intimately related each other.

Of

28

Original ancestor genes

course, genetic codes have the reason forother words, the degeneracy of SNS codons

existing, when both genes and proteins are

expanded a possibility for creation ofpresent.

“original ancestor genes” from antisensesequences (Fig. 8).

During the coevolution between genetic
code and genes, the GNC primeval genetic

Deduced Pathway for Creation of“Original Ancestor Genes” on the
Present Earthcode gradually developed to SNS primitive
genetic code through codon captures, and(GNC)n genes changed their base sequences
to (SNS)n sequences.

Six pairs of SNS

During the coevolution between geneticcodons out of eight can encode the samecode and genes, the SNS primitive genetic

amino acids after base exchanges between G

code gradually developed to the universal

and C at the third codon position, since thosegenetic code through capturing codons withpairs are degenerated at the position.

A and U at the first codon position.

The

In

degeneracy of the SNS codons enabled toparallel, (SNS)n genes evolved to modern

create more easily new “original ancestor

genetic sequences.

genes” from their antisense sequences, as

genes could be created from sense sequences

given in Fig. 8, than GNC codons without

and from antisense sequences through twodegeneracy.

routes as explained above in the case of

Under the SNS primitive

In this case too, newgenetic code, new genes could be created(GNC)n and (SNS)n genes.

from sense sequences and from antisenseof the universal genetic code, it is possible tosequences through two routes as explainedvary many codons among four bases, A, T, G

above in the case of (GNC)n genes.

and C, or among two bases, at the third codon

In

But, in the case(One Original (SNS)n Gene)5'-ggcgccgtcgtcgtcggcgacgccgcc
3'-ccgcggcagcagcagccgctgcggcgg

5'

Sense strand:
Antisense strand :gtcggcgtcggcgtcgacggcgtcggcggcgac-3'
cagccgcagccgcagctgccgcagccgccgctg-5'

3'gcc (Ala)cgg (Gly)
3'

5'

5'

3'

gcg (Ala) the same amino acidcgc (Arg) a different amino acid3'

5'Fig. 8. New gene creation from original (SNS)n gene. New genes were easily produced
from original (SNS)n genes through two routes as similarly as those described in Fig. 6, one
is from sense sequence and the other is from antisense sequence of the original gene.
“Original ancestor genes” could be produced from antisense sequences at a high probability
due to the degeneration of SNS code at the third codon position.

K. Ikehara

29

position without changing amino acids

GNC triplets with phosphodiester bonds (Fig.

encoded, resulting in changing bases at the5).

first codon positions in codons on antisense

evolved to double-stranded (GNC)n genes by

strand and in amino acid replacements in thejoining of GNC triplets on the other side withrange restricted in modified SNS 0th-ordercovalent bonds.

structure of proteins.

genes on double-stranded RNA or DNA, newThen, the single stranded (GNC)n genes

After the formation ofthegenes could be created through two routes,

universal genetic code enabled to create new

one is from sense strands for producing new“original ancestor genes” from their antisense

genes encoding modified and similar proteinssequences much more easily than before.

to the original proteins, and the other is fromThe

degeneracyofcodonsinantisense sequences of the original genes for

Discussion

producing new “original ancestor genes”, asIn this review, I surveyed possible pathways,

given in Fig. 6.

through which new “original ancestor genes”

sense sequences and the second route fromwere created.

theBefore the most primitive

antisense

The first route from thesequencescontributedto(GNC)n genes were created, random lengthy

expansion of protein families and to thearrangements of GNC triplets or GNC

creation of new protein families, respectively.

codons were used in place of the primitive

It can be concluded that, genes in lives on

genes.

At a next step, single-stranded

this planet have been diversified by applying(GNC)n genes were created by joining of

the two routes for producing new genes.
Chemical Evolution(formation of amino acids
from inorganic compounds)[GADV]-Protein World

Fundamental life system(GNC)n Genes

GNC Primeval Genetic Code[GADV]-Proteins(SNS)n Genes

SNS Primitive Genetic Code

SNS-Proteins

Modern GenesThe Universal Genetic CodeModern-ProteinsFig. 9. Possible evolutionary pathway from chemical evolution to the fundamental life
system composed of genes, genetic code and proteins. [GADV]-proteins accumulated bypseudoreplication in [GADV]-protein world synthesized nucleotides and established GNC
primeval genetic code followed by formation of (GNC)n genes. The most primitive
fundamental life system coevolved to the modern life system. Bold arrows, thin arrows andwhite arrows indicate formation processes, evolutionary pathways and flows of genetic
information, respectively.

30

Original ancestor genes(1988 ).

Through coevolution of genetic code andgenes, (GNC)n sequences were evolved to

7.

Ikehara, K.; and Okazawa, E., Unusually(SNS)n genes and modern genes used underbiased nucleotide sequences on sense

theuniversal

evolutionary

genetic

code.

Possiblestrands of Flavobacterium sp. genes

pathwayfromchemicalproducenonstopframesontheevolution to establishment of the fundamental

corresponding antisense strands; Nucl.

life system through [GADV]-protein world

Acids Res. 21 2193-2199 (1993).

are shown in Fig. 9.

8.

Ikehara, K., Possible steps to theemergence of life: The [GADV]-protein

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Communicated by Hiroshi Ueno