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Within-Gene Shine-Dalgarno Sequences Are Not Selected for Function.

Adam J Hockenberry1, Michael C Jewett2,3,4,5,6, Luís A N Amaral2,7

  • 1Department of Integrative Biology, The University of Texas at Austin, Austin, TX.

Molecular Biology and Evolution
|August 8, 2018
PubMed
Summary
This summary is machine-generated.

Most Shine-Dalgarno (SD) sequences within bacterial genes are not functional and are removed by selection. These sequences can be deleterious, potentially causing errors in translation initiation.

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Area of Science:

  • Molecular Biology
  • Evolutionary Biology
  • Genomics

Background:

  • The Shine-Dalgarno (SD) sequence is crucial for translation initiation in bacteria, typically located upstream of start codons.
  • Numerous SD sequence motifs are found within bacterial protein-coding genes, raising questions about their function.

Purpose of the Study:

  • To investigate the functional constraint and evolutionary conservation of SD sequences located within bacterial genes.
  • To determine if these internal SD sequences are under selective pressure.

Main Methods:

  • Comparative evolutionary analysis of SD sequence conservation across Enterobacteriales.
  • Statistical analysis of SD sequence conservation in relation to sequence strength and amino acid constraints.

Main Results:

  • SD sequences within genes are significantly less conserved than expected under neutral evolution.
  • Stronger SD sequences show lower conservation, while weaker SD sequences exhibit some conservation, suggesting selection against strong internal SDs.
  • A depletion of ATG start codons downstream of internal SD sequences was observed, indicating a constraint to prevent erroneous initiation.

Conclusions:

  • The majority of SD sequences within bacterial genes are likely deleterious and are actively removed by negative selection.
  • These findings highlight the evolutionary mechanisms that minimize the risk of aberrant translation initiation within coding regions.