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United States Department of Agriculture

Agricultural Research Service

Title: Evolutionary Implications of Microbial Genome Tetranucleotide Frequency Biases

Authors
item Pride, David - VANDERBILT UNIVERSITY
item Meinersmann, Richard
item Wassenaar, Trudy - ZOTZENHEIM GERMANY
item Blaser, Martin - VANDERBILT UNIVERSITY

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 22, 2002
Publication Date: February 1, 2003
Citation: PRIDE, D.T., MEINERSMANN, R.J., WASSENAAR, T.M., BLASER, M.J. EVOLUTIONARY IMPLICATIONS OF MICROBIAL GENOME TETRANUCLEOTIDE FREQUENCY BIASES. GENOME RESEARCH. 2003.

Interpretive Summary: It is a central dogma of biology that the DNA of an organism reflects its evolution. What determines the direction of evolution is a topic of current research on many fronts. DNA is analyzed for patterns of its constituents for clues to the forces that can bring about those patterns. DNA is made up of nucleotides. This paper shows the results of analyses of bacterial DNA for patterns of short nucleotide groups that are non-random and compared the patterns that are found in the genomes of 23 different organisms. We found patterns that are consistent throughout the length of the genomes. The patterns are species specific and can be used to group the species by their relationship. However, pieces of DNA from viruses that reproduce in bacteria have patterns that are similar to their hosts. In part the patterns reflect what appears to be needed for efficient production of gene products (proteins), but this does not completely account for the observed patterns. The findings were consistent with the idea that evolution of bacteria reflects forces beyond those commonly known as "survival of the fittest."

Technical Abstract: We compared the conservation of nucleotide usage patterns for related organisms by examining representation of DNA tetranucleotide combinations in microbial genomes. For each of 23 organisms studied, tetranucleotide usage was shared between related organisms, and only partially predicted by dinucleotide frequencies or codon distributions. Organisms with GC and AT skews vary in the identity of the tetranucleotide combinations on both sides of their origin of replication. As demonstrated in two E. coli strains, horizontally transmitted DNA did not contribute substantially to the overall tetranucleotide usage frequency-biases of organisms. Individual strains, multiple chromosomes, plasmids, and bacteriophages share tetranucleotide distribution patterns within a species. Grouping these organisms based on tetranucleotide usage resulted in relationships with important differences from those based on 16S rRNA phylogenies. Since these relationships are based on whole genome analyses, they should be considered complementary to phylogenies based on single genetic elements, such as 16S rRNA genes.

Last Modified: 12/18/2014
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