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Related Concept Videos

Evolution of Microbial Genome01:08

Evolution 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.
Genome Size and the Evolution of New Genes03:21

Genome 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.
Genome Size and the Evolution of New Genes03:21

Genome Size and the Evolution of New Genes

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Evolution of New Traits in Microbes01:24

Evolution of New Traits in Microbes

Microorganisms evolve rapidly due to their large population sizes and short generation times, often exhibiting measurable changes within days under laboratory conditions. Natural selection acts on standing genetic variation, enabling the retention and amplification of beneficial traits that confer fitness advantages in changing environments.Adaptive Pigment Regulation in RhodobacterIn Rhodobacter, a genus of purple non-sulfur bacteria, light-harvesting pigments such as bacteriochlorophyll and...
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Bacterial Transcription

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Genomic DNA in Prokaryotes00:46

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Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation
10:41

Conjugative Mating Assays for Sequence-specific Analysis of Transfer Proteins Involved in Bacterial Conjugation

Published on: January 4, 2017

Coevolution of DNA uptake sequences and bacterial proteomes.

W A Findlay1, R J Redfield

  • 1Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario, Canada.

Genome Biology and Evolution
|March 25, 2010
PubMed
Summary

Bacterial genomes contain DNA uptake signal sequences that alter protein sequences. These sequences accumulate in genes after transfer, showing minimal impact on protein function but potentially incurring a high evolutionary cost.

Keywords:
HaemophilusNeisseriaPasteurellaceaecompetencetransformation

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Microbial Genetics

Background:

  • Naturally competent bacteria possess numerous short DNA motifs known as DNA uptake signal sequences (USS) within their genomes.
  • These USS are found in hundreds or thousands of copies, particularly in species like Haemophilus influenzae, Actinobacillus pleuropneumoniae, and Neisseria meningitidis.

Purpose of the Study:

  • To investigate the evolutionary interplay between coding-region USS and the proteomes of three bacterial species.
  • To determine the impact of USS accumulation on protein sequence evolution and gene transfer dynamics.

Main Methods:

  • Comparative genomic analysis of USS distribution in coding sequences across H. influenzae, A. pleuropneumoniae, and N. meningitidis.
  • Analysis of correlations between USS presence, codon usage, gene conservation, and protein functional categories.
  • Comparison of USS-encoded peptides with homologs in related bacteria lacking USS.

Main Results:

  • USS accumulation in coding sequences approximately doubled the frequency of specified tripeptides in the studied genomes.
  • USS presence correlated with preferred codon usage at degenerate positions but showed poor correlation with protein functional categories.
  • Genes lacking homologs also lacked USS, indicating USS accumulation occurs post-gene transfer, not as a driver of distant horizontal gene transfer.
  • USS-encoded amino acids showed similar conservation to other amino acids, suggesting minimal constraint on protein function.
  • USS were preferentially located in poorly conserved genes and amino acid positions.

Conclusions:

  • USS accumulation significantly impacts bacterial proteomes by altering tripeptide frequencies without imposing substantial constraints on protein function.
  • The presence of USS in coding sequences is likely a consequence of gene transfer rather than a driver of it.
  • Maintaining USS in coding sequences may incur a significant evolutionary cost due to the selective pressure needed to mitigate maladaptive mutations.