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Summary Molecular Microbiology (4012687ENR)
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This is the summary of partim 1 of Molecular Microbiology.
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Samenvatting Molecular Microbiology | Jorunn FranckenMolecular Microbiology
Topic 1: Regulation of transcription – Transcription factors
Levels of regulation
MO react to various environmental conditions (nutritional, stress, cell-cell interactions) by sensing
these and employing different modes of regulation in response:
• Transcriptional
• Translational
• Metabolic regulation
2 major approaches to regulate protein function: amount and activity
Figure 1: gene expression and regulation of
protein activity
à Figure 1:
• 5’ UTR = 5 prime untranslated region = short region between start transcription and start
translation (incl ribosome binding site (RBS))
• 3’ UTR = short region between stop codon and transcription terminator
• These are the regions where translational regulation often occurs
• Bottom: mechanisms for regulating protein activity after translation
Transcription
Revision of the components of the basal transcription machinery
The archaeal basal transcription machinery is a simplified version of the eukaryotic RNA polymerase II
machinery
à Figure 2:
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, Samenvatting Molecular Microbiology | Jorunn Francken
• Bac: promoter with -35 and -10 site, sigma factor is not always present (without = core
enzyme), but is needed for the core to bind
• Euk: much larger RNA pol, additional proteins that need to interact, once they are bound,
RNApol can bind, pol has phosphorylated tail, TATA box, 12 subunits
• Archaea: 13 subunits
Figure 2: Transcription
Transcription in Bacteria
Figure 3: Transcription in Bacteria
Bacterial promoter(Figure 3):
• Promoters: initiation sites which pol needs to recognize
• -35 sequence: TTGACA
• -10 sequence (Pribnow box): TATAAT
• Promoters are recognized by sigma
• Transcription occurs in opposite directions on the two different strands of DNA
• Why so many AT? à only 2 H-bonds à easy to “melt/break”
Bacterial RNA polymerase (Figure 4):
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, Samenvatting Molecular Microbiology | Jorunn Francken
• Single RNA polymerase
o Can take different forms and shapes
• Core enzyme:
o Catalyzes RNA synthesis
o 5 subunits: 2 α subunits, β, β’, ω
• Holoenzyme:
o Core enzyme with an associated σ factor
o σ factor (most species have multiple) assists core enzyme by
recognizing promoter Figure 4: Bacterial RNA
• When RNA pol binds promoter à forms closed complex polymerase
• Once bound à RNA pol unwinds DNA à forms open complex
• A region of 16-20 bp unwound DNA becomes “transcription bubble” which moves with the pol
• σ factor dissociates from core enzyme after initiation of transcription
Figure 5: The different steps in transcription
Transcription in Archaea
• The archaeal promoter resembles the eukaryotic
promoter
o Purine-rich factor B recognition element (-33)
§ BRE
§ Upstream of TATA box
o TATA box (-25): 6-8 bp, located upstream of the
transcriptional start site
o Euk: DPE: downstream promoter element
o RNA polymerases are similar and more complex
§ 11-13 subunits Figure 6: Transcription in Archaea
o TBP (TATA-binding protein) recognizes TATA box
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, Samenvatting Molecular Microbiology | Jorunn Francken
§ Is symmetrical à binds in a symmetrical way in minor grove
o TFB (Transcription factor B) binds the TBP-DNA complex and determines the
orientation of transcription by recognizing BRE
o RNA polymerase binds TFB-TBP-DNA complex (= preinitiation complex PIC) and
transcription is initiated
o Some archaea have multiple TBPs and TFBs
Transcription regulation by transcription factors
• Regulation of transcription occurs by the action of regulatory proteins, also
called transcription factors (TFs):
o Sense signals (ligand (small molecules) interaction, posttranslational Figure 7: Transcription in
modifications, …) Archaea (yellow: TBP)
o Bind TF binding sites (TFBSs) in promoter regions on the DNA
o Activate or repress transcription initiation by interacting with basal transcription
machinery
o Regulon = group of genes regulated by the same TF
Transcription factor structure
• Domain architecture of prokaryotic TFs
o Standalone copies of a DNA-binding domain (cI repressor, Fis)
§ Small proteins
o Single-component systems (usually two domains)
§ Single protein combines DNA-binding domain and stimulus sensor module
(directly interacts with small-molecule ligands)
§ Most common
o Two-component systems (consists of two separate proteins)
§ Signal transduction by phosphorylation
§ Prevalent in Bacteria
o Common DNA binding domain: helix-turn-helix, zinc-finger …
Occurrence of transcription factors
• The number of single-component transcription factors in bacterial/archaeal genomes scale
nonlinearly with proteome size
o Complex lifestyles require a higher proportion of TFs and transcription units to better
orchestrate a response to changing conditions
• Figure 8:
o The larger the genome is the more TF are
encoded
o No linear correlation
o Size of the genome is related to the lifestyle of
the organism
o Small genome: parasitic bacteria à they live in
stable conditions inside host cell, rely on the host
Figure 8: Occurrence of transcription factors
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