Related Experiment Video
Updated: Aug 11, 2026
14:49
Associated Chromosome Trap for Identifying Long-range DNA Interactions
Published on: April 23, 2011
Coevolution of DNA-interacting proteins and genome "dialect"
1Institute of Evolution, University of Haifa, Mount Carmel, Haifa, Israel.
Molecular Biology and Evolution
|September 10, 2005
Summary
DNA repair enzyme evolution is closely linked to genome dialect (GD) changes in bacteria, suggesting coevolution driven by factors like stress or horizontal gene transfer. This connection is stronger for DNA repair enzymes than for other proteins.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Genome organization includes species-specific characteristics like genome signature (GS) and compositional spectrum (CS), collectively termed genome dialect (GD).
- Previous studies proposed various genome dialect representatives, but their evolutionary implications remain under investigation.
Purpose of the Study:
- To investigate the correlation between evolutionary distances of bacterial orthologous enzymes and their genome dialect (GD) representatives.
- To test the hypothesis that DNA repair and recombination enzymes exhibit a stronger correlation with GD than other protein families.
Main Methods:
- Quantified genome dialect (GD) representatives, including genome signature (GS) and purine-pyrimidine compositional spectra (PPCS), in Proteobacteria.
- Calculated evolutionary distances between orthologous enzymes involved in DNA repair/recombination and control groups (structural/metabolic).
- Correlated enzyme evolutionary distances with GD distances (PPCS and GS).
Main Results:
- Evolutionary distances of DNA repair and recombination enzymes, particularly from the nucleotide excision repair system, strongly correlated with PPCS and GS distances.
- Orthologous proteins from structural or metabolic processes showed significantly lower correlations between their evolutionary distances and GD distances.
- The bacterial DNA polymerase I, a key DNA repair enzyme, may influence species GD differentiation, potentially driving the observed correlations.
Conclusions:
- A coevolutionary relationship is hypothesized between the structures of DNA repair/recombination enzymes and genome dialects (GDs).
- Changes in DNA repair enzyme structures may be driven by alterations in their DNA substrate, represented by GD differentiation.
- Stress, horizontal gene transfer, and ecological selection are proposed as potential triggers for the coevolution of DNA repair genes and GDs.
Related Concept Videos
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
02:05DNA as a Genetic Template
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
02:54Evolutionary Relationships through Genome Comparisons
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
03:21Genome Size and the Evolution of New Genes
While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
02:05DNA as a Genetic Template
Two structural features of the DNA molecule provide a basis for the mechanisms of heredity: the four nucleotide bases and its double-stranded nature. The Watson-Crick model of double-helical DNA structure, proposed in 1952, drew heavily upon the X-ray crystallography work of researchers Rosalind Franklin and Maurice Wilkins. Watson, Crick, and Wilkins jointly received the Nobel Prize in Physiology or Medicine for their work in 1962. Franklin was, controversially, excluded from the prize for...
01:08Evolution of Microbial Genome
Microbial genome evolution is a highly dynamic process shaped by continual gene gain and loss across species and strains. This genomic flexibility allows microorganisms to adapt rapidly to environmental pressures and interactions with other organisms. Central to understanding this diversity is the distinction between the core and pan genomes.The core genome comprises the genes shared by all sampled strains of a species, representing essential functions needed for fundamental cellular processes.