SURE: Shizuoka University REpository
http://ir.lib.shizuoka.ac.jp/
Title
Evolution without divergence
Author(s)
Tamiya, Nobuo; Yagi, Tatsuhiko
Citation
IUBMB life. 58(5-6), p. 309-311
Issue Date
URL
2006
http://hdl.handle.net/10297/2628
Version
author
Rights
(C)2008 Taylor & Francis Group, an informa business
This document is downloaded at: 2016-03-06T12:14:44Z
more points during evolution (2). We cannot agree with
Evolution without divergence
Dayhoff ’s idea to expand the conclusion to all the living
Nobuo Tamiya and Tatsuhiko Yagi
things. If the conclusion is the case, the ancestor should have
carried an enormously large information, i.e. not only on 20
Dayhoff edited a series books entitled “Atlas of Protein
amino acids, 8 nucleotides and their codons, but also on
Sequence and Structure” (1). She wrote that [1] all cells
homeodomain proteins, which are found commonly in insects
utilize ATP, [2] synthesize, store and break down fats,
and mammals. As for chaperon proteins, which are large
carbohydrates and proteins by similar reactions, [3] live on
hetero-oligomers found in bacteria and mammals, was their
proteins made of same 20 amino acids, [4] synthesize
information present in the ancestor before divergence?
proteins by the same coding system, and [5] utilize similar
Rather, the information to build these proteins must have
ubiquitous compounds, i.e. vitamins and others. She
been collected from various sources of the living world.
concluded that all the living things evolved from a single
It is well established that viruses squeeze into genomes,
common ancestor, which emerged only once. If it is not only
and virus infection is suggested to be significant for
once, the other type creatures died out very soon or were
evolution (4).
eaten up by the common ancestor. According to her, if a
There is a textbook of bacteriology, which recognizes wide
certain type of proteins is found in two species, the original
gene exchange among bacteria (5). There is an idea that
type must have been present in their common ancestor, from
viruses are the fragments of DNA (6, 7).
which they diverged. This is the assumption to deduce the
dendritic divergence map of living creatures.
The idea is widely accepted and quoted in recent textbooks
The ways living things exchange genes are open vertically
and
horizontally,
namely
through
hybridization, symbiosis and infection.
cell
fusion,
sex,
Gene exchange
of biochemistry e.g. by Voet et al. (2) and of biology e.g. by
through sex is efficient even among human beings. Only in
Cain et al. (3).
33 generations, namely in 1000 years, the theoretical
Voet et al. say, however, also that the existence of
number of ancestors can exceed 8×109 ,which is larger than
hemoglobin-like proteins in some species of bacteria is
the world human population. Symbiosis and infection are
evidence of gene transfer from animals to bacteria at one or
often difficult to distinguish. Amoeba, infected with an
1
2
endosymbiont came to require it as cytoplasmic component
phospholipids from enantiomeric ones. It is difficult to
(8, 9).
Margulis’ idea that our cytoplasmic component
imagine a transient cell having membrane composed of
mitochondrion is originally a symbiotic bacterium is now
racemic mixture of sn-1- and sn-3-glycerophospholipids.
widely accepted (10).
The gene exchange between hosts
Rather, primitive cells of archaea and bacteria emerged
and symbionts is an efficient way for evolution because it
separately at some time in early days of earth’s history, and
can happen between remotely related organisms. It is an
evolved independently. Since DNA can be transferred from
efficient way for evolution to transfer related genes together
a cell of one domain to a cell of another domain without
at the same time.
membrane fusion, genetic coding system could coevolve to
The fact that all the known living creatures are composed
use the same code system.
mostly of one group of the optical isomers, e.g. L-amino acids,
There are more examples of metabolic diversity among
is often considered as the evidence for the single ancestor.
three domains of living matters, eucarya, bacteria, and
The authors believe that it is not necessary to think the
procarya. [1] In procarya, isoprenoid biosynthesis proceeds
ancestor or its descendants destroyed the others, but can
not through ordinary pathway via mevalonate, but via a
consider that the continued communication unified the
sugar derivative, 2-C-methyl-D-erythritol (13, 14). [2] Some
creatures to the present form.
bacteria use polyphosphate instead of ATP (NTP) for their
The similarity of cell components, metabolites, and the
energy metabolism (15, 16, 17), and some archaea use ADP
pathways to produce and break down them is often quoted
rather than ATP to phosphorylate sugar metabolites in their
as the evidence for the single ancestor theory. There are,
glycolytic pathway (18, 19). [3] At least three different
however, many cases against it. In archaea, plasma
pathways are known for heme biosynthesis (20, 21).
membrane
from
Zorzopulos (22) proposed that the birth of each domain was
sn-1-phosphatidate instead of ordinary sn-3-phosphatidate
an independent event consisting in the genetic isolation of a
from which bacterial and eucaryal membrane phospholipids
particular cell from a very diverse pool of "primitive cells",
are synthesized (11, 12). If archaea and bacteria diverged
and that within each domain, branching was a consequence
from a common ancestral cell, it must have occurred that one
of sporadic events of fusion between two cells of different
of domain precursor cells began to synthesize its membrane
phylogenetic lineages, followed by DNA recombination and
components
are
3
synthesized
4
cell wall regeneration. This proposal has to be modified to
The difference in the conversation languages is a big
allow some degree of DNA recombination among cells
problem we human beings are confronting. Living things
belonging to different domains for the coding system to be
might have nearly overcome the difficulty through 3.5 billion
unified.
years of communication and they almost succeeded to
It is said that a diverse biomass exists in the deep-sea
construct the Tower of Babel.
This is why we can
hydrothermal vents (23, 24). It may reveal there exist many
synthesize human proteins, such as insulin and growth
more new pathways of metabolism.
hormone (31,32, 33) in the bacterial systems. There are,
On the “universal codon system” there are reports on the
however, unsuccessful cases among yeast species due to the
cases that do not agree with its universality. In addition to
code difference (25, 26) The introduction of a new property
the discrepancy between codons between mammalian cells
is due to the variation in gene by mutation and other
and their mitochondria, similar cases are found also in some
mechanisms.
species of yeasts (25, 26). The living things may be
namely vectors (i.e. phages, plasmids) and enzymes (i.e.
approaching to the universal codon system after 3.5 billion
restriction enzymes, ligases), may also work in nature for
years of communication.
gene-transfer.
The tools we use for gene-engineering,
Selenocysteine, which uses codon UGA, one of the stop
When one of the authors gave talk on the idea in an
codons, may be now beginning to distribute as the 21st amino
international meeting (34), one from the audience said that
acid (27, 28). Tryptophan, which has the lowest average
if living creatures exchanged information so widely, all of
occurrence in proteins as compared to the other 19 amino
them would have become a homogeneous mess. This will
acids (2, 29) and has only one codon (UGG), might have
never happen because the size of information, a living
become distributed later than the other amino acids because
creature can carry, is limited; it cannot be very different
of its complicated structure and indispensable character as a
from its direct vertical ancestor.
protein component. From the sequence comparison, Syvanen
In conclusion, it is not necessary to think that all living
was
things evolved from a common ancestor, which emerged only
introduced after the three domains of living matter
once. Instead, gene-exchange can explain most of the
“diverged” from one another.
characteristics, which present organisms share in common.
(30)
concluded
that
tryptophan
5
synthase
gene
6
The authors published essentially the same idea in 1985
biological weapons. Med. Hypotheses 65, 868-872
(35). In the report the authors pointed out the discrepancy
(7) Bush, R.M. (2004) Influenza as a model system for
of the phylogenetic trees constructed based on different
studying the cross-species transfer and evolution of the
proteins of closely related species.
SARS coronavirus. Philos. Trans. R. Soc. Lond. B359,
The authors are grateful to their late Professor Shiro
Akabori for his continued encouragement by letters on the
idea mentioned above.
1067-1073
(8) Jeon, K.W. (1972) Development of cellular dependence on
infective organisms: micrurgical studies in amoebas.
Science 176, 1122-1123
References
(9) Jeon, K.W. and Jeon, M.S. (1976) Endosymbiosis in
(1) Dayhoff, M.O. (1972) Atlas of Protein Sequence and
Structure,
Vol.5,
National
Biomedical
Research
Foundation, Georgetown, Maryland
(2) Voet, D., Voet, J.G. and Pratt, C.W. (2005) Fundamentals
of Biochemistry, 2nd ed, p.3, p.78, p.186, John Wiley & Sons,
amoebae:
Recently
established
endosymbionts
have
become required cytoplasmic components. J. Cell. Physiol.
89, 337-44.
(10) Margulis, L. (1981) Symbiosis in Cell Evolution, W.H.
Freeman and Company, San Francisco, California
(11) Koga, Y., Kyuragi, T., Nishihara, M. and Sone, N. (1998)
Hoboken, New Jersey
(3) Cain, M.L., Damman, H., Lue, R.A. and Yoon, C.K. (2002)
Did archaeal and bacterial cells arise independently from
Discover Biology, 2nd. ed. Sinauer Associates Inc. and W. W.
noncellular precursors? A hypothesis stating that the
Norton & Company, Sunderland, Maryland
advent of membrane phospholipid with enantiomeric
(4) Anderson, N.G. (1970) Evolutionary significance of virus
infection. Nature 227, 1346-1347
(5) Sonea, S. and Panisset, M. (1983) A New Bacteriology,
p.22 Jones and Bartlett, Boston, Massachusetts
(6) Bubanovic, I., Najman, S. and Andjelkovic, Z. (2005)
Origin and evolution of viruses: escaped DNA/RNA
sequences as evolutionary accelerators and natural
7
glycerophosphate backbones caused the separation of the
two lines of descent. J. Mol. Evol. 46, 54-63
(12) Daiyasu, H., Hiroike, T., Koga, Y. and Toh, H. (2002)
Analysis of membrane stereochemistry with homology
modeling
of
sn-glycerol-1-phosphate
dehydrogenase.
Protein Engineering 15, 987-995
(13) Kuzuyama, T. (2002) Mevalonate and nonmevalonate
8
pathways for the biosynthesis of isoprene units. Biosci.
of
Biotechnol. Biochem. 66, 1619-1627
hyperthermophilic archaeon Pyrococcus furiosus. J. Biol.
(14) Puan, K.J., Wang, H., Dairi, T., Kuzuyama, T., and
Morita, C.T. (2005) fldA is an essential gene required in
a
novel
ADP-dependent
isoprenoid biosynthesis. FEBS Lett. 579, 3802-3806
typhimurium:
S.,
Yoshida,
A.
and
Koike,
M.
the
(20) Wang, L. Y., Brown, L., Elliott, M. and Elliott, T. (1997)
Regulation
Mudd,
from
Chem. 270, 30453-30457
the 2-C-methyl-D-erythritol 4-phosphate pathway for
(15)
glucokinase
of
heme
activity
biosynthesis
of
in
glutamyl-tRNA
Salmonella
reductase
(1958)
(HemA) is greatly elevated during heme limitation by a
Polyphosphate as accumulator of phosphorus and energy.
mechanism which increases abundance of the protein. J.
J. Bacteriol. 75, 224-235
Bacteriol. 179, 2907-2914
(16) Szymona, M. and Ostrowski, W. (1964) Inorganic
(21) Ishida, T., Yu, L., Akutsu, H., Ozawa, K., Kawanishi, S.,
Mycobacterium phlei.
Seto, A., Inubushi, T. and Sano, S. (1998) A primitive
polyphosphate
glucokinase
of
Biochim. Biophys. Acta 85, 283-295
pathway of porphyrin biosynthesis and enzymology in
(17) Bobyk, M.A., Afinogenova, A.V., Dudinskaya, M.V.,
Lambina, V.A. and Kulaev, I.S. (1980) Detection of
polyphosphates
and
enzymes
of
polyphosphate
metabolism in Bdellovibrio bacteriovorus. Zentralbl.
Bakteriol. Naturwiss. 135, 461-466
S.W., Stams, A.J. and de Vos, W.M. (1999) Molecular and
characterization
Archaea and Eucarya and of major taxa within them: a
hypothesis. Rev. Argent. Microbiol. 35, 175-182
New Jersey
(24) Kimura, H., Sugihara, M., Yamamoto, H., Patel, B.K.,
hyperthermophilic
Kato, K. and Hanada, S. (2005) Microbial community in a
archaeon Pyrococcus furiosus. J. Biol. Chem. 274,
geothermal aquifer associated with the subsurface of the
21023-21028
Great Artesian Basin, Australia. Extremophiles 9, 407-414
from
the
the
Hydrothermal Vents, Princeton Univ. Press, Princeton,
ADP-dependent
phosphofructokinase
of
(22) Zorzopulos, J. (2003) Birth of the domains Bacteria,
(23) Van Dover, C.L. (2000) The Ecology of Deep-Sea
(18) Tuininga, J.E., Verhees, C.H., van der Oost, J., Kengen,
biochemical
Desulfovibrio vulgaris. Proc. Natl. Acad. Sci. 95, 4853-8
(19) Kengen, S.W., Tuininga, J.E., de Bok, F.A., Stams, A.J.
(25) Pesole, G., Lotti, M., Alberghina, L. and Saccone, C.
and de Vos, W.M. (1995) Purification and characterization
(1995) Evolutionary origin of nonuniversal CUGSer codon
9
10
in some Candida species as inferred from a molecular
phylogeny. Genetics 141:903-907
Biotechnol. 84, 175-185
(33) Gray, G.L., Baldridge, J.S., McKeown, K.S., Heyneker,
(26) Zimmer, T. and Schunck, W.H. (1995) A deviation from
H.L. and Chang, C.N. (1985) Periplasmic production of
the universal genetic code in Candida maltosa and
correctly processed human growth hormone in Escherichia
consequences for heterologous expression of cytochromes
coli:
P450 52A4 and 52A5 in Saccharomyces cerevisiae. Yeast
interchangeable. Gene 39:247-254
Natural
and
bacterial
signal
sequences
are
(34) Tamiya, N. (1987) in Progress in Venom and Toxin
11, 33-41
(27) Böck, A., Forchhammer, K., Heider, J. and Baron, C.
Research eds. Gopalakrishnakone, P. and Tan, C.K.,
(1991) Selenoprotein synthesis: an expansion of the
Faculty of Medicine, National University of Singapore,
genetic code. Trends Biochem. Sci. 16, 463-467
p.137
(28) Stadtman, T.C. (1996) Selenocysteine. Annu. Rev.
Biochem. 65, 83-100
evolution: Sequence comparison of some proteins from
(29) Doolittle, R.F. in Fassman, G.D. (Ed.) Predictions of
Protein
Structure
(35) Tamiya, N. and Yagi, T. (1985) Non-divergence theory of
and
the
Principles
of
snakes and bacteria. J. Biochem. 98, 289-303
Protein
Conformation. Plenum Press.
Authors
(30) Syvanen, M. (2002) On the occurrence of horizontal gene
transfer among an arbitrarily chosen group of 26 genes. J.
Correspondence to be made
Dr. Nobuo Tamiya, Emeritus Professor, Tohoku University
Mol. Evol. 54, 258-266
(31) Chan, S.J., Weiss, J., Konrad, M., White, T., Bahl, C., Yu,
Dr. Tatsuhiko Yagi, Emeritus Professor, Shizuoka University
S.D., Marks, D. and Steiner, D.F. (1981) Biosynthesis and
periplasmic
segregation
of
human
proinsulin
in
Escherichia coli. Proc. Natl. Acad. Sci. 78, 5401-5405
(32) Winter, J., Neubauer, P., Glockshuber, R. and Rudolph,
R. (2001) Increased production of human proinsulin in the
periplasmic space of Escherichia coli by fusion to DsbA. J.
11
12