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. 2002 Oct 1;30(19):4264-71.
doi: 10.1093/nar/gkf549.

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes

Igor B Rogozin  1 , Kira S Makarova, Darren A Natale, Alexey N Spiridonov, Roman L Tatusov, Yuri I Wolf, Jodie Yin, Eugene V Koonin
Affiliations

Congruent evolution of different classes of non-coding DNA in prokaryotic genomes

Igor B Rogozin et al. Nucleic Acids Res. .

Abstract

Prokaryotic genomes are considered to be 'wall-to-wall' genomes, which consist largely of genes for proteins and structural RNAs, with only a small fraction of the genomic DNA allotted to intergenic regions, which are thought to typically contain regulatory signals. The majority of bacterial and archaeal genomes contain 6-14% non-coding DNA. Significant positive correlations were detected between the fraction of non-coding DNA and inter- and intra-operonic distances, suggesting that different classes of non-coding DNA evolve congruently. In contrast, no correlation was found between any of these characteristics of non-coding sequences and the number of genes or genome size. Thus, the non-coding regions and the gene sets in prokaryotes seem to evolve in different regimes. The evolution of non-coding regions appears to be determined primarily by the selective pressure to minimize the amount of non-functional DNA, while maintaining essential regulatory signals, because of which the content of non-coding DNA in different genomes is relatively uniform and intra- and inter-operonic non-coding regions evolve congruently. In contrast, the gene set is optimized for the particular environmental niche of the given microbe, which results in the lack of correlation between the gene number and the characteristics of non-coding regions.

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Figures

Figure 1
Figure 1
Three types of gene pairs (M, methionine; *, stop codon).
Figure 2
Figure 2
Distribution of distances in convergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 2
Figure 2
Distribution of distances in convergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 2
Figure 2
Distribution of distances in convergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 2
Figure 2
Distribution of distances in convergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 3
Figure 3
Distributions of distances in divergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 3
Figure 3
Distributions of distances in divergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 3
Figure 3
Distributions of distances in divergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 3
Figure 3
Distributions of distances in divergent gene (COG) pairs in (A) E.coli, (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 4
Figure 4
Distribution of distances in unidirectional gene pairs in E.coli within documented operons and within conserved gene (COG) pairs (A); distributions of distances in conserved unidirectional gene (COG) pairs in (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 4
Figure 4
Distribution of distances in unidirectional gene pairs in E.coli within documented operons and within conserved gene (COG) pairs (A); distributions of distances in conserved unidirectional gene (COG) pairs in (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 4
Figure 4
Distribution of distances in unidirectional gene pairs in E.coli within documented operons and within conserved gene (COG) pairs (A); distributions of distances in conserved unidirectional gene (COG) pairs in (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 4
Figure 4
Distribution of distances in unidirectional gene pairs in E.coli within documented operons and within conserved gene (COG) pairs (A); distributions of distances in conserved unidirectional gene (COG) pairs in (B) C.acetobutylicum, (C) Synechocystis and (D) T.volcanium.
Figure 5
Figure 5
Correlation between the fraction of non-coding DNA and the median distance between genes in conserved unidirectional gene pairs (intra-operonic distances).
Figure 6
Figure 6
Correlation between the median distance between genes in conserved unidirectional gene pairs (intra-operonic distances) and the median distance in convergent and divergent gene pairs (inter-operonic distances).
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