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GC-content of genomes - a trap for cladists?

forsdyke forsdyke at post.queensu.ca
Fri Feb 26 13:15:25 EST 1999

Steffen Schmidt wrote:
> I'am looking for ideas and papers about the following statement which is possibly wrong (but why?):

> ... all these comparision algorithm do rely on
> the fact that there is no selection on the level of the nucleotides. 
> But one believes also that thermophilic organism do need a higher GC-content
> in order to live in their various habitats. 
Dr. Schmidt,
            Some thermophilic organisms have a low GC% (e.g. A.
aeolicus), so high GC% is not a sine-qua-none of hyperthermic existence.
There is evidence that rRNA (not mRNAs and thus their corresponding
genes) adapt to high temperature by increasing GC% (summarized in the
following Letter to the Editor, which Dr. G. Bernardi declined in 1997
to publish in the Journal of Molecular Evolution). 

Sincerely, Donald Forsdyke

                       LETTER TO THE EDITOR

Neutralism versus selectionism: no correlation between optimum growth
temperature and genome G+C content does not refute the selectionist

By Donald R. Forsdyke
Department of Biochemistry, Queen's University, Kingston, Ontario,
Canada K7L3N6

Abstract. Galtier and Lobry (1997; J Mol Evol 44:632-636) compared the
optimum growth temperatures of various prokaryotes with the G+C content
of their genomic DNA and of various non-mRNA RNA species (e.g. ribosomal
RNAs). Since GC bonds confer greater stability on nucleic acid secondary
structure than AT bonds, their data strongly suggest that an increase of
G+C content is needed for the stabilization at high temperature of rRNA
secondary structure (stem-loops), but not of DNA secondary structures.
The authors propose that "any secondary structure that must endure at
high temperatures requires a high G+C content", so that "a high
proportion" of stem-loop "secondary structures in bacterial genomes is
unlikely". Thus, the fact that Chargaff's parity rule (%A=%T, %G=%C)
applies to single-stranded DNA (as to single-stranded RNA), is held to
be "poorly explained" on the basis of an evolutionary pressure on DNA to
form stem-loops (as proposed by Forsdyke 1995; J Mol Evol 41:573-581).
Rather the parity rule would be explained by "neutral directional
mutational pressure" (Lobry, 1995; J Mol Evol 40:326-330). However, "any
secondary structure" includes the classical duplex DNA secondary
structure. This is likely to exist at high temperatures, and presumably
requires "other physiological adaptations" than an increase in G+C
content. Such adaptations might also apply to DNA stem-loop secondary
structure. Thus, in this context selectionist arguments are no less
probable than neutralist arguments.  

Key words:  Chargaff's parity rule - G+C content - Secondary structure 

A single-stranded nucleic acid with the potential to form stem-loop
secondary structures should tend to follow Chargaff's parity rule
(%A=%T, %G=%C). This is because Watson-Crick base pairing is involved in
the formation of stems, and might also be involved in intrastrand
loop-loop interactions which would further stabilize the secondary
structures. The potential for genomic DNA in the classical duplex form
to extrude stem-loop secondary structures is widely distributed in the
DNA of all species studied (Murchie et al. 1992; Forsdyke, 1995a), and
involves both extragenic DNA, and intragenic DNA (Forsdyke, 1995b,c;
   Thus, the compositions of single-stranded DNAs tend to follow the
parity rule (Forsdyke, 1995c), and the RNAs transcribed from them might
also tend to follow the rule. Indeed, mRNAs, which in prokaryotes with
compact genomes are more likely to be reflective of total genomic
structure and base composition than rRNAs (Muto and Osawa 1987), can be
folded using energy-minimization algorithms into very compact stem-loop
secondary structures (Jaeger et al. 1990).  
    Ribosomal RNAs also form compact stem-loop secondary structures and
so tend to follow Chargaff's parity rule. In prokaryotes optimal growth
temperature (Topt) correlates positively with the G+C content of rRNA,
but not of genomic DNA (Fiala and Stetter, 1986; Dalgaard and Garret
1993). This has been confirmed by Galtier and Lobry (1997), who propose,
quite plausibly, that the increase in G+C content of rRNA is required to
stabilize stem-loop structures under hyperthermic conditions. Free of
coding constraints, yet required to form part of the presumably very
precise structure of ribosomes, rRNA might be under greater pressure to
accept mutations which increase G+C content than most mRNAs. 
    However Galtier and Lobry (1997) also propose that "any secondary
structure that must endure a high temperature requires a high G+C
content" (my italics). This is manifestly incorrect, since the authors
themselves report that "no correlation was found between genomic G+C
content and Topt". It follows that the classical secondary structure of
duplex DNA is likely to be stabilized by what the authors refer to as
"other physiological adaptations"; these might include increased
association of DNA with basic polyamines (Oshima et al. 1990), and
relaxation of supercoiling (Friedman et al. 1995).
     In the context of possible DNA stem-loop secondary structures,
Galtier and Lobry (1997) conclude that "a high proportion of [such]
secondary structures in bacterial genomes is unlikely" so that the fact
that Chargaff's parity rule applies to single-strands of DNA "is poorly
explained" (by Forsdyke 1995c) on this basis. Instead, the authors
propose that Chargaff's parity rule tends to apply to single-stranded
DNA because of neutral directional mutation pressure (Lobry, 1995;
Sueoka, 1995). 
    The arguments of Galtier and Lobry (1997) rest on the assumption
that stem-loop structures in rRNAs are comparable with stem-loop
structures extruded from duplex DNA.  However, there is no reason to
believe that "other physiological adaptations" at high temperatures
cannot stabilize both the classical DNA duplex secondary structure and
DNA stem-loop secondary structures. The energetics of helix (stem)
formation is essentially the same whether DNA has a classical duplex
secondary structure or a stem-loop secondary structure (Murchie et al.
1992). As we currently understand it, the latter structure would be
required only under certain clearly defined, but selectively important,
circumstances (i. e. for recombination repair; Forsdyke, 1996b;
Kleckner, 1997). The enduring DNA secondary structure would be the
classical duplex form.   
    Thus, Galtier and Lobry (1997) do not make an adequate case for
neutral directional mutational pressure as an explanation for the
applicability of Chargaff parity rule to single-stranded DNA. In the
context of their data, selectionist arguments are no less probable than
neutralist arguments.  The data indicating no selective advantage of
high genomic G+C content at high temperature (Fiala and Stetter 1986;
Galtier and Lobry 1997), appear to support the neutralist argument that
variations in genomic G+C content have arisen by drift in small
populations (Filipski 1990). However, the data are also consistent with
the selectionist argument that genomic G+C content is too important
merely to follow the dictates of temperature, since its primary role is
to respond to the G+C contents of other species in order to prevent
inter-species recombination (Forsdyke, 1996b). Other selectionist
arguments have been advanced by Bernardi (1993).

Bernardi G (1993) The vertebrate genome. Isochores and evolution. Mol
Biol Evol 10:186-204
Dalgaard JZ, Garrett A (1993) Archaeal hyperthermophile genes. In: Kates
M et al. (eds) The biochemistry of Archaea (Archaebacteria). Elsevier
Science, Amsterdam, pp 	535-562
Filipski J (1990) Evolution of DNA sequences. Contributions of
mutational bias and selection to the origin of chromosomal compartments.
Adv Mut Res 2:1-54
Forsdyke DR (1995a) A stem-loop "kissing" model for the initiation of
recombination and the origin of introns. Mol Biol Evol 12:949-958
Forsdyke DR (1995b) Conservation of stem-loop potential in introns of
snake venom phospholipase A2  genes. An application of FORS-D analysis.
Mol Biol Evol 12: 1157-1165
Forsdyke DR (1995c) Relative roles of primary sequence and (G+C)% in 
determining the hierarchy of frequencies of complementary trinucleotide
pairs in DNAs of different species. J Mol Evol 41:573-581
Forsdyke DR (1996a) Stem-loop potential in MHC genes: a new way of
evaluating positive Darwinian selection. Immunogenetics 43:182-189
Forsdyke DR (1996b) Different biological species "broadcast" their DNAs
at different (C+G)% "wavelengths". J Theor Biol 178:405-417
Friedman SM, Malik M, Drlica K (1995) DNA supercoiling in a
thermotolerant mutant of Escherichia coli. Mol Gen Genet 248:417-422
Galtier N, Lobry JR (1997) Relationships between genomic G+C content,
RNA secondary structures, and optimal growth temperature in prokaryotes.
J Mol Evol 44:632-636
Jaeger JA, Turner DH, Zuker M (1990) Predicting optimal and suboptimal
secondary structure for RNA.  Meth Enzymol 183:281-317
Kleckner N (1997) Interactions between and along chromosomes during
meiosis. Harvey Lectures 91:21-45
Lobry JR (1995) Properties of a general model of DNA evolution under
no-strand-bias conditions. J Mol Evol 40:326-330
Murchie AIH, Bowater R, Aboul-Ela F, Lilley DMJ (1992) Helix opening
transitions in supercoiled DNA. Biochem. Biophys. Acta 1131:1-15 
Muto A, Osawa S (1987) The guanine and cytosine content of genomic DNA
and bacterial evolution. Proc Natl Acad Sci USA 84:166-169
Oshima T, Hamasaki N, Uzawa T, Friedman SM (1990) Biochemical functions
of unusual polyamines found in the cells of extreme thermophiles. In:
Goldembeg SH, Algranati ID (eds) The biology and chemistry of
polyamines. Oxford University Press, New York, pp 1-10
Sueoka N (1995) Intrastrand parity rules of DNA base composition and
usage biases of synonymous codons. J Mol Evol 40:318-325

Further info: http://post.queensu.ca/~forsdyke/evolutio.htm

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