Abundant oligonucleotides common to most bacteria

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Bacterial genomes exhibit oligonucleotide composition biases beyond G+C content.
• Oligonucleotide patterns carry phylogenetic signals, aiding species identification.
• Previous studies focused on short oligomers; mid-sized oligomer distributions across prokaryotes remain under-assessed.

Purpose of the Study:

• To survey overrepresented mid-length oligomers across all prokaryotes.
• To analyze global distributions of these oligomers, normalized for base composition.
• To investigate the evolutionary and functional significance of these DNA sequences.

Main Methods:

• Surveyed overrepresented mid-length oligomers in prokaryotic genomes.
• Employed zero and second-order Markov models for normalization.
• Analyzed structural parameters and protein interactions of identified oligomers.

Main Results:

• Identified an ancient set of conserved, overrepresented oligomers (homopurines and homopyrimidines) in nearly all prokaryotes.
• These oligomers are adenine-rich or cytosine-rich, with specific guanine or cytosine inclusions.
• Oligomers do not favor coding regions and suggest roles in DNA structure and protein binding, forming rigid B-DNA prone to triple helix formation.

Conclusions:

• Homopurine and homopyrimidine oligomers possess distinct, unusual structural features.
• Their high abundance across prokaryotic lineages suggests a conserved, non-neutral role in genome organization.
• These findings highlight the evolutionary maintenance of specific oligonucleotide functions in prokaryotes.