gene regulation - prokaryotes

the genotype and phenotypes of bacteria

• The potential phenotypes of bacteria is carried in their DNA 

• The genotype is the potential to show different features 

• Phenotype is the expression of genetic traits in the genotype 

• The features shown by the bacteria are their phenotype 

• Phenotypes change depending on the environment 

the bacterial genome

• The majority of bacterial genomes are circular (Streptomyces) are linear 

• Linear in size 

• Extra-chromosomal DNA & plasmids give bacteria extra properties 

  • Some associated with antibiotic resistance 

  • Plasmids can be transferred between bacterial cells (horizontal gene transfer) 

variation in bacterial genomes

• Vary in size and number 

• Generally, a linear relationship between genome size and number of genes 

• Genes tightly packed 

  • Almost no introns 

  • Little space between gene coding regions 

• On average one open reading frame (ORF) per 1-1.2 kb 

• On average 20-40% of every bacterial genome is unique to that organism 

  • Functions of these genes are often unknown 

how to create a phenotype

• Bacteria sense their environment to ensure their 'transcriptome' is optimal for their environment 

• There are 3 major stages of transcription, all of which can be regulated 

  • Initiation 

    • Requires a sigma factor that recognises the –10 and –35 region 

    • It allows RNA polymerase to know where to initiate transcription 

    • Opens DNA to enable transcription 

    • Housekeeping sigma factor (transcription of key genes for bacterial cell function) 

    • There are alternative sigma factors (e.g. stress responses) 

• Elongation 

  • Not at a uniform speed 

  • Speed and pausing is determined by the DNA sequence being transcribed and RNA secondary structure 

  • Proteins can be bound to the DNA to block transcription 

• Termination  

  • Terminators are punctuation marks within the DNA sequence, defining where transcription stops 

  • Is intrinsic 

  • Rho dependent termination 

• Transcription is catalysed by a single RNAP 

  • RNAP core enzyme is composed of five sub-units  

    • 2 x beta 

    • 2 x alpha 

    • 1 x omega 

bacterial messenger RNAs

• No nucleus through which mRNAs need to be transported 

• Effectively no processing of mRNAs before translation 

  • Do not have methyl-G caps or poly-A tails 

  • Do have NAD capping 

• Newly made (nascent) mRNA transcripts are translated 

  • Thus bacteria are able to rapidly synthesise proteins 

• Relatively less stable than eukaryotic mRNA 

  • Half-life of bacterial mRNA is roughly 2 mins 

  • It is 4-24 hours for eukaryotes 

transcription factors

• Turn gene expression on or off 

• Bind to DNA  

  • Normally near the start of the transcriptional start site 

• Recognise specific sequences in the DNA 

  • Gene expression specificity 

• Either help or hinder binding of RNA polymerase 

• Respond to environmental signals 

• Positive control (with activator proteins) 

• Negative control (with repressor proteins) 

• Negative repressible operons

transcription factors

positive control - with activator proteins

• RNA polymerase can only bind to the promoter region if an activator protein binds to a site near the promoter 

• If the activator does not bind to the DNA, the RNA polymerase cannot bind and transcription does not occur 

transcription factors

negative control - with repressor proteins

• The natural state of the DNA allows the RNA polymerase complex to be recruited and transcription takes place 

• If the repressor protein binds to the DNA, it inhibits recruitment of RNA polymerase and transcription does not occur 

transcription factors

negative repressible operons

• On until turned off 

• No corepressor 

  • Repressor is inactive 

  • Transcription occurs 

• Corepressor present 

  • Repressor binds to corepressor 

  • Causes conformational change in shape 

  • Forms an active complex 

  • Transcription is blocked 

activation of transcription - LuxR

• Quorum sensing – molecular system to monitor population density 

• Bacteria produce autoinducer molecules 

  • Can be a peptide or a small molecule 

  • Concentration dependent 

    • Linked to density of the population 

    • Population becomes quorate to co-ordinate changes in behaviour 

• This is recognised by a transcription factor – LuxR 

  • In the absence of the molecule, the DNA binding site is revealed and LuxR can recognise transcription factor binding sites 

  • Transcription of gene

tryptophan repression of transcription

• TetR acts as a transcriptional repressor 

• Binds to tetO boxes (specific sequences) 

• Blocks interaction of RNA polymerase 

• When tetracycline is added binds to TetR 

• Causes conformational change in shape so can no longer bind to tetO 

• RNA polymerase binds 

repression of transcription

controlling iron levels

• 70% of iron in the human body is in the form of heme 

• In other environments iron is a rare nutrient 

• Essential for many important biological processes 

• Too much iron can be dangerous for cells 

  • Causes DNA damage due to oxidative stress 

• Fur is a transcription factor that detects iron availability 

  • Binds to Fe2+ 

• When iron binds to Fur 

  • Complex binds to Fur box 

  • No transcription 

  • Happens in an iron abundant environment 

• When iron does not bind to Fur 

  • Not complimentary to Fur box 

  • RNA polymerase binds to DNA 

  • Transcription occurs 

• Fur regulates Shiga Toxin production 

  • Shiga toxin is produced in the intestinal tract 

  • Oxygen availability is variable, leading to changes in iron availability 

  • If oxygen is absent, Fe2+ is present 

  • If oxygen is present, iron is oxidised to fe3+ 

  • Fur is bound to, and transcription occurs 

antisense small RNA (sRNA)

• Regulatory RNA, complementary to specific mRNA, used to reduce translation