Another engineering principle characterization
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Another engineering principle: Characterization. A stupid engineering joke:. A physicist, a mathematician and an engineer were each asked to establish the volume of a red rubber ball.

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Another engineering principle: Characterization.

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Another engineering principle:Characterization.

A stupid engineering joke:

  • A physicist, a mathematician and an engineer were each asked to establish the volume of a red rubber ball.

  • The physicist immersed the ball in a beaker full of water and measured the volume of the displaced fluid. The mathematician measured the diameter and calculated a triple integral. The engineer looked it up in his Red Rubber Ball Volume Table.

  • Basically, engineers want to know the characteristics of their parts and devices.

  • They list these characteristics in tables, books and files.

  • Want a beam that can hold 1000 lbs? Look it up.

But first

  • More on bacterial transcription and promoters and such

Genome Network Project, Nature Genetics, 2009

Environmental change



Turn gene(s) on/off


Proteins to deal with

new environment

Transcriptional Control

  • Very important to:

  • express genes when needed

  • repress genes when not needed

  • Conserve energy resources; avoid expressing unnecessary/detrimental genes

RNA Structures Vary

  • RNA more like proteins than DNA:

    structured domains connected by more flexible domains, leading to different functions

  • e.g. ribozymes – catalytic RNA


  • RNA polymerase

  • Transcription factors

  • Promoter DNA

    • RNAP binding sites

    • Operator – repressor binding

    • Other TF binding sites

      Start site of txn is +1

α α ββ’σ


  • RNA polymerase

    • 4 core subunits

    • Sigma factor (σ)–

      determines promoter


    • Core + σ = holoenzyme

    • Binds promoter sequence

    • Catalyzes “open complex” and transcription of DNA to RNA

RNAP binds specific promoter sequences

  • Sigma factors recognize consensus

    -10 and -35 sequences

RNA polymerase promoters



Deviation from consensus -10 , -35 sequence leads to

weaker gene expression

Bacterial sigma factors

  • Sigma factors are “transcription factors”

  • Different sigma factors bind RNAP and recognize specific -10 ,-35 sequences

  • Helps melt DNA to expose transcriptional start site

  • Most bacteria have major and alternate sigma factors

  • Promote broad changes in gene expression

    • E. coli 7 sigma factors

    • B. subtilis 18 sigma factors

  • Generally, bacteria that live in more varied environments have more sigma factors

Sigma factors







Extreme heat shock, unfolded proteins

E. coli can choose between 7 sigma factors and about 350

transcription factors to fine tune its transcriptional output

An Rev Micro Vol. 57: 441-466T. M. Gruber

Lac operon control

  • Repressor binding prevents RNAP binding promoter

  • An activating transcription factor found to be

  • required for full lac operon expression: CAP (or Crp)




lac operon

no mRNA

Cofactor binding alters conformation

  • Crp binds cAMP, induces allosteric changes





Cooperative binding of Crp and RNAP

Binds more stably than either protein alone

Interaction of CAP-cAMP, RNA Pol and

DNA of lac control region

lac operon – activator and repressor

CAP = catabolite

activator protein

CRP = cAMP receptor


Cis-acting sequence is activator (or CAP) binding site.

cAMP signals low glucose

activator binding-site

lac operon off


lac operon very weakly on

lac operon fully induced

The ara Operon

•another example of operon that has both positive

and negative regulation

•araB, A, and D encode the 3 arabinose

metabolizing enzymes

•araC encodes the control protein AraC which is both

a positive regulator (in the presence of arabinose) and

a negative regulator (in the absence of arabinose).

•cAMP-CAP complex also acts as a positive regulator

Organization of the ara operon

Control of the ara Operon I - Negative


•When arabinose is absent, the AraC protein acts as

a negative regulator.

•AraC acts as a dimer, and causes the DNA to loop.

Looping brings the I1 and O2 sites in proximity to one


•One AraC monomer binds to I1 and a second monomer

binds to O2.

•Binding of AraC prevents RNA Pol from binding to

the PBAD promoter

Control of the ara Operon II - Positive


•When arabinose is present, it binds to AraC and changes

AraC conformation

•An arabinose-AraC dimer complex binds preferentially

to I1 and I2, and NOT to O2 which causes ‘opening’

of the loop. This allows RNA Pol to bind to PBAD.

•If glucose levels are low, cAMP-CAP complex binds

to Pc.

•Active transcription occurs.

Control can also happen at the Ribosome binding site

What about the terminator?

  • Termination sequence has 2 features:

  • Series of U residues

  • GC-rich self-complimenting region

  • GC-rich sequences bind forming stem-loop

  • Stem-loop causes RNAP to pause

  • U residues unstable, permit release of RNA chain

One type of characterization is Tuning

  • Some promoters bind RNAPs better so they are stronger

  • Some RBSs make mRNA that bind better to the ribosome so they are stronger

  • And some are weaker…


  • By mixing and matching promoters and RBS parts we can have genetic devices that work at various levels

  • Weak Promoter + weak RBS = weak device

  • Strong Promoter + strong RBS = strong device

  • Weak Promoter + strong RBS =

  • Medium Promoter + medium RBS =

  • The synthetic biologists got together and decided on a reference promoter against which others would be measured.

  • Much like the standard meter.

Why would synthetic biologists want to be able to tune a system/device?

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