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Related Concept Videos

The Eukaryotic Promoter Region02:40

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The eukaryotic promoter region is a segment of DNA located upstream of a gene. It contains an RNA polymerase binding site, a transcription start site, and several cis-regulatory sequences.  The proximal promoter region is located in the vicinity of the gene and has cis-regulatory sequences and the core promoter. The core promoter is the binding site for RNA polymerase and is usually located between -35 and +35 nucleotides from the transcription start site. The distal promoter regions are...
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RNA polymerase (RNAP) carries out DNA-dependent RNA synthesis in both bacteria and eukaryotes. Bacteria do not have a membrane-bound nucleus. So, transcription and translation occur simultaneously, on the same DNA template.
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Unlike eukaryotes, bacteria use a single RNA Polymerase (RNAP) to transcribe all genes. The different subunits of bacterial RNAPhave distinct functions. The multisubunit structure of the bacterial RNAP helps the enzyme to maintain catalytic function, facilitate assembly, interact with DNA and RNA, and self-regulate its activity.
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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.
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Prokaryotic Gene Structure and Organization01:28

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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...
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Prokaryotic Transcriptional Activators and Repressors01:58

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The organization of prokaryotic genes in their genome is notably different from that of eukaryotes. Prokaryotic genes are organized, such that the genes for proteins involved in the same biochemical process or function are located together in groups. This group of genes, along with their regulatory elements, are collectively known as an operon. The functional genes in an operon are transcribed together to give a single strand of mRNA known as polycistronic mRNA.
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Predicting bacterial promoter function and evolution from random sequences.

Mato Lagator1,2, Srdjan Sarikas2,3, Magdalena Steinrueck2

  • 1School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, United Kingdom.

Elife
|January 26, 2022
PubMed
Summary
This summary is machine-generated.

Scientists developed a biophysical model to predict bacterial gene expression from any DNA sequence. This reveals that functional promoters are common, suggesting gene regulation evolves rapidly.

Keywords:
E. coliRNA polymeraseadaptive evolutioncomputational biologyevolutionary biologygene regulationgenotype-phenotype mappromotersystems biology

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Area of Science:

  • * Molecular Biology
  • * Biophysics
  • * Bioinformatics

Background:

  • * Predicting biological function from DNA sequence remains a significant challenge.
  • * Current methods are limited to local sequence variations, not global prediction.
  • * Understanding promoter function is crucial for gene regulation.

Purpose of the Study:

  • * To develop a biophysical model for predicting bacterial promoter function from any DNA sequence.
  • * To quantify the prevalence of functional promoter sequences in random DNA.
  • * To investigate the evolutionary dynamics of promoter emergence.

Main Methods:

  • * Construction and analysis of random mutant libraries for bacterial promoters.
  • * Development of a biophysical model incorporating features of sigma-70 (σ70) binding.
  • * Experimental and theoretical estimation of gene expression levels from various sequences.

Main Results:

  • * 10-20% of random sequences can function as promoters.
  • * Approximately 80% of non-expressing sequences are one mutation away from a functional promoter.
  • * Selection acts against σ70-RNA polymerase binding sites in intergenic regions due to their pervasiveness.

Conclusions:

  • * The emergence of promoters is not a rate-limiting step in gene regulatory evolution.
  • * Promoter sequences evolve more rapidly than previously understood.
  • * Mechanistic models enhance prediction accuracy and reveal evolutionary insights.