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Investigations of oligonucleotide usage variance within and between prokaryotes.

Bohlin J, Skjerve E, Ussery DW - PLoS Comput. Biol. (2008)

Bottom Line: Among the results found was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i.e., information in prokaryotic genomes is encoded in short oligonucleotides.Pronounced DNA compositional differences were found both within and between AT-rich and GC-rich genomes.The differences found between AT-rich and GC-rich genomes may possibly be attributed to lifestyle, since tetranucleotide usage within host-associated bacteria was, on average, more dissimilar and less biased than free-living archaea and bacteria.

View Article: PubMed Central - PubMed

Affiliation: Norwegian School of Veterinary Science, Oslo, Norway.

ABSTRACT
Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di- to tetranucleotides). We wanted to assess the statistical information potential of different DNA 'word-sizes' and explore how oligonucleotide frequencies differ in coding and non-coding regions. In addition, we used oligonucleotide frequencies to investigate DNA composition and how DNA sequence patterns change within and between prokaryotic organisms. Among the results found was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i.e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than in GC-rich and free-living genomes, and this variation was mainly located in non-coding regions. Bias (selectional pressure) in tetranucleotide usage correlated with GC content, and coding regions were more biased than non-coding regions. Non-coding regions were also found to be approximately 5.5% more AT-rich than coding regions, on average, in the 402 chromosomes examined. Pronounced DNA compositional differences were found both within and between AT-rich and GC-rich genomes. GC-rich genomes were more similar and biased in terms of tetranucleotide usage in non-coding regions than AT-rich genomes. The differences found between AT-rich and GC-rich genomes may possibly be attributed to lifestyle, since tetranucleotide usage within host-associated bacteria was, on average, more dissimilar and less biased than free-living archaea and bacteria.

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Ratio of observed divided by expected OUD values.The vertical axis shows the ratio of observed divided by expected OUD values for each chromosome sorted with respect to genomic GC content from left to right on the horizontal axis. The ratio test measures how observed oligonucleotide usage varies within chromosomes (red line) and coding regions (blue line) compared with expected based on GC content. Rising ratio values above 1 (vertical axis) means increased observed variance compared with expected. The dotted lines represent 99% prediction intervals.
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pcbi-1000057-g005: Ratio of observed divided by expected OUD values.The vertical axis shows the ratio of observed divided by expected OUD values for each chromosome sorted with respect to genomic GC content from left to right on the horizontal axis. The ratio test measures how observed oligonucleotide usage varies within chromosomes (red line) and coding regions (blue line) compared with expected based on GC content. Rising ratio values above 1 (vertical axis) means increased observed variance compared with expected. The dotted lines represent 99% prediction intervals.

Mentions: Difference in tetranucleotide usage within genomes was supported by a ratio test where observed tetranucleotide usage variance within genomes was divided by expected tetranucleotide variance approximated by nucleotide frequencies. From Figure 5 it can be observed that considerably less variation was detected in the coding regions (blue line) compared with chromosomes containing both coding and non-coding regions (red line) with the following regression equations:YO_E and YCO_E (response) are the ratios of observed divided by expected OUD values for genomes and coding regions respectively, while XGC represents mean global GC content (predictor).


Investigations of oligonucleotide usage variance within and between prokaryotes.

Bohlin J, Skjerve E, Ussery DW - PLoS Comput. Biol. (2008)

Ratio of observed divided by expected OUD values.The vertical axis shows the ratio of observed divided by expected OUD values for each chromosome sorted with respect to genomic GC content from left to right on the horizontal axis. The ratio test measures how observed oligonucleotide usage varies within chromosomes (red line) and coding regions (blue line) compared with expected based on GC content. Rising ratio values above 1 (vertical axis) means increased observed variance compared with expected. The dotted lines represent 99% prediction intervals.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2289840&req=5

pcbi-1000057-g005: Ratio of observed divided by expected OUD values.The vertical axis shows the ratio of observed divided by expected OUD values for each chromosome sorted with respect to genomic GC content from left to right on the horizontal axis. The ratio test measures how observed oligonucleotide usage varies within chromosomes (red line) and coding regions (blue line) compared with expected based on GC content. Rising ratio values above 1 (vertical axis) means increased observed variance compared with expected. The dotted lines represent 99% prediction intervals.
Mentions: Difference in tetranucleotide usage within genomes was supported by a ratio test where observed tetranucleotide usage variance within genomes was divided by expected tetranucleotide variance approximated by nucleotide frequencies. From Figure 5 it can be observed that considerably less variation was detected in the coding regions (blue line) compared with chromosomes containing both coding and non-coding regions (red line) with the following regression equations:YO_E and YCO_E (response) are the ratios of observed divided by expected OUD values for genomes and coding regions respectively, while XGC represents mean global GC content (predictor).

Bottom Line: Among the results found was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i.e., information in prokaryotic genomes is encoded in short oligonucleotides.Pronounced DNA compositional differences were found both within and between AT-rich and GC-rich genomes.The differences found between AT-rich and GC-rich genomes may possibly be attributed to lifestyle, since tetranucleotide usage within host-associated bacteria was, on average, more dissimilar and less biased than free-living archaea and bacteria.

View Article: PubMed Central - PubMed

Affiliation: Norwegian School of Veterinary Science, Oslo, Norway.

ABSTRACT
Oligonucleotide usage in archaeal and bacterial genomes can be linked to a number of properties, including codon usage (trinucleotides), DNA base-stacking energy (dinucleotides), and DNA structural conformation (di- to tetranucleotides). We wanted to assess the statistical information potential of different DNA 'word-sizes' and explore how oligonucleotide frequencies differ in coding and non-coding regions. In addition, we used oligonucleotide frequencies to investigate DNA composition and how DNA sequence patterns change within and between prokaryotic organisms. Among the results found was that prokaryotic chromosomes can be described by hexanucleotide frequencies, suggesting that prokaryotic DNA is predominantly short range correlated, i.e., information in prokaryotic genomes is encoded in short oligonucleotides. Oligonucleotide usage varied more within AT-rich and host-associated genomes than in GC-rich and free-living genomes, and this variation was mainly located in non-coding regions. Bias (selectional pressure) in tetranucleotide usage correlated with GC content, and coding regions were more biased than non-coding regions. Non-coding regions were also found to be approximately 5.5% more AT-rich than coding regions, on average, in the 402 chromosomes examined. Pronounced DNA compositional differences were found both within and between AT-rich and GC-rich genomes. GC-rich genomes were more similar and biased in terms of tetranucleotide usage in non-coding regions than AT-rich genomes. The differences found between AT-rich and GC-rich genomes may possibly be attributed to lifestyle, since tetranucleotide usage within host-associated bacteria was, on average, more dissimilar and less biased than free-living archaea and bacteria.

Show MeSH