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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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Average oligonucleotide usage deviance within prokaryotic chromosomes (OUD).Each archaeal and bacterial chromosome is sorted on the horizontal axis with increasing GC content from left to right, with corresponding OUD values on the vertical axis. The red and blue lines represent OUD scores for whole chromosomes and coding regions, respectively. Smaller OUD values mean more homogeneous chromosomes in terms of tetranucleotide usage. The surrounding dotted lines indicate 99% prediction intervals.
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pcbi-1000057-g004: Average oligonucleotide usage deviance within prokaryotic chromosomes (OUD).Each archaeal and bacterial chromosome is sorted on the horizontal axis with increasing GC content from left to right, with corresponding OUD values on the vertical axis. The red and blue lines represent OUD scores for whole chromosomes and coding regions, respectively. Smaller OUD values mean more homogeneous chromosomes in terms of tetranucleotide usage. The surrounding dotted lines indicate 99% prediction intervals.

Mentions: From Figure 4 it can be observed that OUD scores were lower in coding regions (blue line) than in chromosomes containing both coding and non-coding regions (red line). Genomic OUD scores were progressively decreasing with increasing GC content indicating that tetranucleotide patterns in non-coding regions become progressively more similar with growing GC content. The following regression equations were obtained:The response-functions YOUD and YCOUD represent OUD scores in genomes and coding regions, respectively, while the predictor XGC is GC content.


Investigations of oligonucleotide usage variance within and between prokaryotes.

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

Average oligonucleotide usage deviance within prokaryotic chromosomes (OUD).Each archaeal and bacterial chromosome is sorted on the horizontal axis with increasing GC content from left to right, with corresponding OUD values on the vertical axis. The red and blue lines represent OUD scores for whole chromosomes and coding regions, respectively. Smaller OUD values mean more homogeneous chromosomes in terms of tetranucleotide usage. The surrounding dotted lines indicate 99% prediction intervals.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1000057-g004: Average oligonucleotide usage deviance within prokaryotic chromosomes (OUD).Each archaeal and bacterial chromosome is sorted on the horizontal axis with increasing GC content from left to right, with corresponding OUD values on the vertical axis. The red and blue lines represent OUD scores for whole chromosomes and coding regions, respectively. Smaller OUD values mean more homogeneous chromosomes in terms of tetranucleotide usage. The surrounding dotted lines indicate 99% prediction intervals.
Mentions: From Figure 4 it can be observed that OUD scores were lower in coding regions (blue line) than in chromosomes containing both coding and non-coding regions (red line). Genomic OUD scores were progressively decreasing with increasing GC content indicating that tetranucleotide patterns in non-coding regions become progressively more similar with growing GC content. The following regression equations were obtained:The response-functions YOUD and YCOUD represent OUD scores in genomes and coding regions, respectively, while the predictor XGC is GC content.

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