The dynamic structure of the prokaryotic information Hans V. Westerhoff and friends Molecular Cell...
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The dynamic structure of the The dynamic structure of the prokaryotic information prokaryotic information Hans V. Westerhoff and friends Hans V. Westerhoff and friends Molecular Cell Physiology, Institute for Molecular Cell Biology Molecular Cell Physiology, Institute for Molecular Cell Biology and Swammerdam Institute for Life Sciences, BioCentrum and Swammerdam Institute for Life Sciences, BioCentrum Amsterdam Amsterdam
The dynamic structure of the prokaryotic information Hans V. Westerhoff and friends Molecular Cell Physiology, Institute for Molecular Cell Biology and
The dynamic structure of the prokaryotic information Hans V.
Westerhoff and friends Molecular Cell Physiology, Institute for
Molecular Cell Biology and Swammerdam Institute for Life Sciences,
BioCentrum Amsterdam
Slide 2
Molecular Microbiology: DNA supercoiling IMC
Slide 3
International Systems Biology Conference 2004 in
Heidelberg
Slide 4
Molecular Microbiology: DNA supercoiling Here we are ..
zBillons of bps, hundreds of transcriptomes, some proteomes, parts
of the metabolome, even a phenome or two further . and . zLeena
Peltonen: hyperlipidemia: >10 factors involved; cannot be
tracked down even with island populations zSvante Pbo: substantial
expression divergence without functional consequences zJoseph
Nadeau: Different mouse strains show wide difference in homeostasis
in response to folate depletion zStefan Schreiber: >600 genes
differentially expressed between (Crohn) in inflamed mucosa;
dissection does not allow to identify the multifactorial etiology
z, i.e.: we still do not understand..
Slide 5
I will tell you what you know already .. But what we did not
yet live up to..
Slide 6
Molecular Microbiology: DNA supercoiling Life arises not just
in the isolated molecules but in their communication Jan Steen
Slide 7
Molecular Microbiology: DNA supercoiling zTV >>>
transistors; zCell >>> molecules; zOrganism >>
cells; zEcosystem >> organisms Important properties emerge
from the interactions/integration How do molecules and cells do
this ? The subject of System Biology The subject of System
Biology
Slide 8
Molecular Microbiology: DNA supercoiling How scientific
conferences differ from (some) lectures.. zTalk by scientist A
zScientist B listens zAsks a question and makes A think and respond
zA and B go home zDo a new experiment and make a new discovery
zNext time the talks of both A and B go further zThe essence: zA
influences A through a dynamic action through B zIt is important
that both A and B are dynamically responsive
Slide 9
What is System Biology? The properties that arise in
interactions .. Through the dynamic- dynamic modes
Slide 10
The coin of System Biology has two sides The System differs
from the sum of the molecules (without interactions) .. The
molecules behave differently in the system
Slide 11
Molecular Microbiology: DNA supercoiling Both system and
molecules are different
Slide 12
Molecular Microbiology: DNA supercoiling Look at the
system
Slide 13
Molecular Microbiology: DNA supercoiling or look at the
molecule. in interaction
Slide 14
Molecular Microbiology: DNA supercoiling DNA: Dynamic molecule
in the system. Really???? ?
Slide 15
Molecular Microbiology: DNA supercoiling The primary and
secondary structure of B-DNA zHydrophobic interior zHydrophilic
exterior zBase pairing zMajor and minor groove zRight-handed helix
zPitch: 3.4 nm; 10.4 bps z1 bp: 0.33 nm
Slide 16
Molecular Microbiology: DNA supercoiling Static? Or?
zHydrophobic interior zHydrophilic exterior zBase pairing zMajor
and minor groove zRight-handed helix zPitch: 3.4 nm; 10.4 bps z1
bp: 0.33 nm
Slide 17
Molecular Microbiology: DNA supercoiling The twist zTw= number
of times the two strands rotate around each other y(when one
follows the ds DNA through space) zB-form DNA: 1/10.4 basepairs zE.
coli 4.6 million basepairs, I.e. zTw = 0.44 million
Slide 18
Molecular Microbiology: DNA supercoiling Three known secondary
structures of DNA left-handed!
Slide 19
Molecular Microbiology: DNA supercoiling A, B and Z DNA;
differences zZ: left-handed zB: minor and major groove zPitch (10,
10.4 and 12 bps) zTwist
Slide 20
Molecular Microbiology: DNA supercoiling The twist zB-form DNA:
1/10.4 basepairs zE. coli 4.6 million basepairs, I.e. zTw = 0.44
million zA-form DNA: 1/10.0 basepairs zTw=0.44 million zZ-form DNA:
-1/12 basepairs: zTw=-0.38 million
Slide 21
Molecular Microbiology: DNA supercoiling Special primary
structure: circular DNA zSome DNAs are circular zThe 5 and 3 ends
of each strand are covalently closed zBecause of the twist of the
strands, zthis causes the strands to be linked
Slide 22
Molecular Microbiology: DNA supercoiling Linking number zThe
number of times the one strand has been caught by the other) zHow
many times does one need to cut, strand pass and reseal to liberate
the two strands zFlat circle: Lk = Tw zSupercoiled circle Lk Tw 1 3
4 5 6 7 8 9 2
Slide 23
Molecular Microbiology: DNA supercoiling For a flat circle
Linking and twisting are not independent zLk = Tw zFlat pBR322
circle: Lk = Tw = 419 zNow: increase the Lk by 1 zLk=420 zNow Tw
also 420 if circle remains flat
Slide 24
Molecular Microbiology: DNA supercoiling Changing the
topology
Slide 25
Molecular Microbiology: DNA supercoiling 1 3 4 5 6 7 8 9 2 4 1
3 2 6 7 89 5 10 9 2 3 4 1 7 8 1 6 5 Link +1 Let go Change Lk, Tw
and Wr
Molecular Microbiology: DNA supercoiling zStrand cutting
required to change Lk zDNA molecule can itself exchange Tw with Wr
zDNA likes standard Tw zWr (supercoiling) tends to change when Lk
is changed zWr: supercoiling, cruciforms zLk, not Wr can be
measured by extracting the DNA Implications
Slide 28
Molecular Microbiology: DNA supercoiling Same writhe; two
conformations toroidal plectonemic
Slide 29
Molecular Microbiology: DNA supercoiling How can the cell
change supercoiling zWr: nucleosomes, DNA binding proteins zTw:
intercalating agents, ionic strength, RNA polymerase zLk: nicking
then closing: yTopoisomerase I: single strand nick yTopisomerase
II; double strand nick yTopoisomerases and transcription zNote:
yTw, Lk and Wr: always 2 change together ychange in Lk can be
measured and therefore this is usually called change in
supercoiling
Slide 30
Molecular Microbiology: DNA supercoiling How can the cell
change supercoiling zLk: nicking then closing: yTopoisomerase I:
single strand nick
Slide 31
Molecular Microbiology: DNA supercoiling How can the cell
change supercoiling zLk: nicking then closing: yTopoisomerase II:
double strand nick, passage of double stranded DNA, closure
Slide 32
Molecular Microbiology: DNA supercoiling How does the cell
bring about supercoiling zBacterial Topoisomerase II (gyrase):
reduces Lk zLk=Tw+Wr zCauses negative Wr zSupercoiling is negative:
zLk deficit: Lk