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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Gene Evolution - Fast or Slow?02:05

Gene Evolution - Fast or Slow?

The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
In contrast, regions which code...
Prokaryotic Gene Structure and Organization01:28

Prokaryotic Gene Structure and Organization

Prokaryotic genomes exhibit a streamlined organization of coding and non-coding regions essential for gene expression and protein synthesis. While coding regions contain the genetic instructions for proteins or functional RNAs, non-coding regions regulate the precise transcription and translation of these genes.Coding Regions: Proteins and RNAsThe primary coding regions, known as structural genes, include sequences transcribed into messenger RNA (mRNA) and ultimately translated into...
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

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.
Cis-regulatory Sequences02:02

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

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Identifying Amino Acid Overproducers Using Rare-Codon-Rich Markers
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Evolutionary pressures on simple sequence repeats in prokaryotic coding regions.

Wei-Hsiang Lin1, Edo Kussell

  • 1Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA.

Nucleic Acids Research
|November 30, 2011
PubMed
Summary
This summary is machine-generated.

Simple sequence repeats (SSRs) are mutation hotspots. Certain bacteria utilize SSRs in coding DNA to control gene activity for survival, a process called phase variation.

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Following the Dynamics of Structural Variants in Experimentally Evolved Populations
04:52

Following the Dynamics of Structural Variants in Experimentally Evolved Populations

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Area of Science:

  • Genomics
  • Microbial genetics
  • Evolutionary biology

Background:

  • Simple sequence repeats (SSRs) are known indel mutational hotspots within genomes.
  • In prokaryotes, SSRs can drive phase variation, a survival mechanism involving reversible gene activity switching.

Purpose of the Study:

  • To analyze SSR variability and distribution in prokaryotic coding regions.
  • To understand how repeat type and genomic position influence SSR mutation rates and density.
  • To investigate evolutionary pressures shaping SSR distribution in protein-coding sequences.

Main Methods:

  • Analysis of SSRs across 42 prokaryotic species' genomes.
  • Characterization of SSR density and variability along protein sequences (N→C termini).
  • Use of codon-shuffling algorithms to assess evolutionary pressures on SSRs.

Main Results:

  • Repeat type significantly impacts indel mutation rates; highly mutable SSR types are genome-wide avoided.
  • Coding sequences exhibit U-shaped SSR density curves, with suppression in protein middles and enrichment near termini.
  • This U-shape is often attributable to biophysical protein structure constraints.
  • Pathogenic bacteria show SSR enrichment near N-termini beyond structural expectations.

Conclusions:

  • SSR distribution in prokaryotic genomes is influenced by both mutation rates and evolutionary selection.
  • Biophysical constraints shape general SSR patterns, but specific species, especially pathogens, tune SSRs for enhanced phase variation.
  • Over-enrichment of SSRs near N-termini in some bacteria facilitates phase variation by increasing frameshift probability.