lecture 3 Flashcards
how is the chromosome compacted?
Compacted in an orderly and hierarchical fashion with a functional three dimensional form to allow replication , recombination, segregation, and transcription
what is the genetic map?
organization of the chromosome within the bacteial cell
what controls the chromosome architecture?
Controlled by specialized proteins
what are some methods for visualizing the bacterial chromosome?
cryo electron tomography
super-resolution microscopies
what is the structure of the chromosome?
Overall curved shape
- bundles at the central core and low-debsuty regions
what are the features of cryo electron tomography?
bacteria within native condition
has biological context
is high resolution
Low contract
is just a snapshot
what are the features of super-resolution microscopies?
The bacteria are live
Has functional context
it is fast and easy
Has low resolution
hard labeling
what is the structural organisation of the bacterial chromosome?
- The chromosome is compacter in an orderly and hierarchical fashion in lockstep with DNA replication
- It is not enclosed by a membrane
- The organization of the chromosome within the bacterial cell recapitulates the genetic map
- The chromosome is organized at different scales
what are CIDs?
Chromosome interaction domains
what are features the chromosome interaction domains?
- insulated from flanking regions, self interactions
- 10^2-10^3 kbp
- boundaires between CIDs: highly expressed genes
- HEG- house keeping genes (ribosomal gene cluster)
how does the number of CIDs differ?
depending on growth conditions
what are the important positions within the bacterial chromosome?
- replication (oriC) - one pole
The replication terminus (ter) - opposite pole
pole-anchoring proteins - Left and right chomosomal arms
what determines chromosome configuration?
Chromosome configuration is different in different bacteria and depends on the growth conditions
what does the ori-ter pattern determine?
Each daughter cell inherits a full copy of the genome
what happens during replication to the DNA?
During replication the new DNA moves to its relative position
what shape are bacterial chromosome?
Most bacterial chromosomes are circular but some are linear
what is the role of MatP in E.coli?
Keeps Ter in a compacted form
MatP binds to 13-bp matS sites present exclusively in the ~800-kb Ter macrodomain
MatP binds the matS site as a dimer
interacts with membranes
what is the function of NAPs?
They govern DNA organization
how is eukaryotic DNA organized?
Genomic DNA is condensed using histones (identical repeating octamers)
how is bacterial DNA organized?
organized plectonemic supercoiled using specific proteins
what are NAPs?
nucleoid-associated proteins
what are the structural maintenance complexes of chromosomes?
- ‘hinge’ dimerization domain
- an antiparallel coiled-coil ‘arm’ extending between the hinge and head domains
- ATPase ‘head’ domain
- Kleisin-interacting winged tandem elements (kite)
what are DNA loop extrusion mechanisms?
- embracing a pair of DNA segments in a signle ring
- dimerization of two rings
what are the structure of histone-like nucleoid structuring protein (H-NS)?
-small polypeptide; binds the DNA minor groove using a C-terminal arginine hook motif
- AT rich segments
- head-to-head: H-NS-DNA filaments
- Tail-to-tail DNA-H-NS-DNA bridges
- can occlude RNAP binding sites or transcription activators-> gene epxression
what are the features of heat stable protein form E.coli U93 strain?
- two subunits (alpha and beta) -> homo and heterodimers
- Flexible hinge: range of different angles
- abundant: 30,000 copies/cell
- can make octamers (spiral structures)
what do integration host factors do?
make a hairpin in the DNA strand at 160 degrees
what causes DNA light bending?
Fis
what is Fis?
Factor for inversion stimulation
what are the features of Fis?
- highly expressed gene during rapid cell division
- conserved in most gram-negative bacteria
- bending the DNA by 50-60 degrees
- stable, long-lived nucleoprotein complexes
- can regulated transcription
what can modulate the structure of NAPs?
additional proteins
what induces supercoiling?
RNAP induces +/- supercoiling
how is dsDNA topologically constrained?
dsDNA circular molecule is topologically constrained- no rotation of the free ends
- genome organizes in plectonemic supercoils constrained by NAPs
what is plectonemic supercoiling?
a cut in one domain will only relax that domain and not others
how do topoisomerases bind and cut DNA?
One DNA strand- type 1
both DNA strands- type II
what happens when supercoiled DNA unravels?
once it uncoils it will reform in a circle
what mediates chromosome condensation?
condensation mediated by supercoiling and NAPs
what is bulk chromosome segragation?
the orderly compaction of the replicated sisters along adjacent DNA segments
what facilitates the origin of segregation?
the origin of segregation is facilitated by a highly conserved partitioning system
how to topoisomerases work in chromosome segragation?
Topoisomerases (IV) enriched ahead of replication forks and transcription bubbles
how do environmental conditions affect DNA organization?
- the chromosome structure changes with environmental conditions
- Conformational changes induced by ligands
Mg stabilizes H-NS helix conformation - temperature reduces H-NS oligomerizations and dissociation from DMA
- Usually NAPs present in lower level in starved cells
DNA adopts a crystalline structure
what are important things to remember?
- bacterial chromosome is compacted
- bacterial chromosome is hierarchically organized
- various methods are used to study DNA organization
- NAPs are modelling the DNA
- NAPs expression and structure respond to environmental stimuli
how does Mg affect chromosomes?
stabilizes H-NS helix conformation
