Download A general trend for invertebrate mitochondrial genome evolution

A general trend for invertebrate mitochondrial genome evolution
Haidong Tan1
Masaharu Seno2
[email protected]
1
2
[email protected]
Biotechnology division, Dalian Institute of Chemical Physics, Academy of Chinese Sciences, 457
Zhongshan Rd, Dalian, 116023, China
Laboratory of Nano-Biotechnology，Department of Medical and Bioengineering Science，Graduate
School of Natural Science and Technology，Okayama University，3.1.1 Tsushima-Naka, Kita, Okayama
700-8530, Japan
Abstract: Exploring DNA and protein evolution is very basic research. Here, 60 sets of invertebrate
mitochondria were selected; whose entire genome sequences, protein-coding DNA and proteins sequences
evolution were studied. The results were interesting. For the whole mitochondrial genome evolution, the
AT content is increasing and GC is reducing during the life evolution going. The net ratio of AT content
creation to GC deletion was about 4/3. For protein-coding DNA evolution, the TG contents were
increasing and AC contents were consistently reducing. These results were firstly reported. For
mitochondrial genome protein evolution, ten amino acids losers and ten amino acids gainers were found,
which was difference with previous reports.
Keywords: invertebrate mitochondria, genome evolution, protein-coding DNA evolution, protein
evolution
1 Introduction
Genome evolution study is very basic research recently. It is routinely known that extant DNA and
proteins are equilibrium and their evolution is stationary and reversible: reciprocal fluxes of nucleotide
base and amino acids substitutions are equal. However, we also know that each organism will be affected
by nature selection and a general trend for amino acids and nucleotides change should be existed. In 2005,
Jordan et al reported the trends of amino acid changes were similar in 15 taxa representing Bacteria,
Archaea, and Eukaryota [2]. However, the general trend for the change of protein-coding DNA was not
found and the conclusion was still debated today [3].
For the study, mitochondria may be the potential candidate. Mitochondria are the sites of aerobic
respiration, and are the major energy production center in eukaryotes. Invertebrate mitochondrial
genomes are circular, about 16 kb in length, and typically encode 13 proteins used for energy production,
as well as 22 tRNAs and 2 ribosomal RNAs. The low mutation rate in invertebrate mtDNA sequence
makes these genomes useful for the study of small genome evolution. Therefore, we studied the entire
geome sequences, protein-coding DNA and proteins sequences evolution here.
2 Method and Results
All 60 available triplets of complete eukaryotic mitochondrial genomes-for which the divergence of the
DNA sequences of genome from the sister genomes was within 1-20%, and the outgroup sister genomes
divergence was 30%. All the data (whole mitochondrial genome, protein-coding DNA and protein
sequences) were downloaded from the NCBI [1]. All the triplets of orthologues, identified sequences were
identified using the reciprocal best-hit approach and aligned by Clustal W through Vector NTI 10. In each
three-sequence alignment, only the sites carrying the same bases or amino acids between outgroup and
one of the sisters but difference with another was considered. Thus, the amino acids or nucleotide bases
flow could be seen by three-taxa method.
We analyzed 60 sets of three-way alignments of closely related invertebrate mitochondrial genomes,
protein-coding DNA and protein sequences. At sites where the outgroup and one of the sister genomes
carry the same amino acid, while the other sister genome carries a different one, the base or amino acid
ancestral for the sister genomes can be inferred.
After creation/deletion substitution accounts, ten amino acids were found to be losers: Asn (the ratio of
creation/deletion substitution:0.5), Leu (0.58), Glu (0.65), Ile (0.67), Gln (0.7), Trp (0.75), Lys (0.78), Thr
(0.82), Pro (0.89) and Gly (0.98) (Fig. 1), and ten amino acids were gainers: Cys (3), Asp (1.7), Val (1.63),
Arg (1.56), Met (1.53), Ala (1.52), Ser (1.5), Phe (1.38), His (1.12) and Tyr (1.06) (Fig. 1). These results
were obviously different with previous reports four strong ‘losers’ (Pro, Ala, Glu and Gly) and five strong
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‘gainers’ (Cys, Met, His, Ser and Phe) [2].
For the whole mitochondrial genome evolution, we found that the AT content is increasing and GC is
reducing during the life evolution going. The net ratio of AT content creation to GC deletion was about
4/3. For protein-coding DNA evolution, the creation/deletion substitution ratio of the both nucleotide
bases T and G contents were 3 and 2.7 respectively, so the TG content were increasing. On the other hand,
the creation/deletion substitution ratio of the both nucleotide bases A and C contents were 0.72 and 0.55
respectively, so their contents were consistently reducing.
Figure 1. Normalized difference between the number of substitutions creating and removing amino acids
in 60 sets of mitochondrial genome proteins. The individual capital letters stand for 20 kinds of amino
acids.
3 Discussions
Here, we studied the entire mitochondrial genome evolution, protein-coding DNA evolution and its
proteins evolution. A general trend for their evolution was found: AT content is increasing and GC content
is reducing in the whole genome, while TG content is increasing and AC content is reducing in its
protein-coding DNA. We conjectured all the results might be caused by the nucleotide bases substitutions
cytosine to thymine, which is almost three fold higher than other nucleotide bases substitutions. Actually,
cytosine methylation in DNA contributed to the nucleotide bases substitutions C to T, which was widely
existed in vertebrates. It is generally believed that T.G mismatches created by the hydrolytic deamination
of 5-methylcytosines (5meC) are intermediates in the mutagenic pathway [4].
For mitochondrial genome protein evolution, the change trend was different with previous report [2]. We
guessed that might be caused by the different percent contents of different amino acid. After comparison,
we find no thus direct relation for the evolution. For example, the percent content of Asn was almost
fourfold less than that of Leu, but Asn was reducing faster than that of Leu. Obviously, mitochondrial
genomes only occupied a little part in all the genomes, and they had their own special characters.
Therefore, next interesting work still would be carried out: the chloroplast genome evolution.
References
[1] http://www.ncbi.nlm.nih.gov/genomes/OrganelleResource.cgi?opt=organelle&taxid=33208
[2] Jordan, I. K., Kondrashov, F. A., Adzhubei, I. A., Wolf, Y. I., Koonin, E. V., Kondrashov, A. S., and
Sunyaev, S.,A universal trend of amino acid gain and loss in protein evolution, Nature
433:633-638, 2005
[2] McDonald, J. H., Apparent trends of amino Acid gain and loss in protein evolution due to nearly
neutral variation, Molecular biology and evolution 23: 240-244, 2006
[3] Lutsenko, E., and Bhagwat, A. S., Principal causes of hot spots for cytosine to thymine mutations
at sites of cytosine methylation in growing cells. A model, its experimental support and
implications, Mutat Res 437: 11-20, 1999
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