week 6+7 - bacterial chromosome organisation Flashcards
What is Bacterial Chromosome Organisation
chatgpt
Bacterial chromosomes are highly compacted structures that allow millimetres of DNA to fit into a tiny cell (about 1–2 µm in size), while still remaining accessible for replication and transcription.
key features of organisation:
Nucleoid
chatgpt
Region in the cytoplasm where DNA is compacted; no membrane-bound nucleus
key features of organisation:
Loops/Domains
chatgpt
Chromosome is organized into topologically independent domains (loops)
key features of organisation:
Negative Supercoiling
chatgpt
Maintains DNA in a compact state while promoting access to the DNA sequence
key features of organisation:
NAPs (Nucleoid-Associated Proteins)
chatgpt
Non-specific DNA-binding proteins (e.g., HU, Fis, H-NS) help shape the nucleoid
key features of organisation:
Macromolecular Crowding
chatgpt
Dense cytoplasm promotes DNA condensation via entropic effects
key features of organisation:
Topoisomerases
chatgpt
Enzymes that regulate DNA supercoiling (e.g., DNA gyrase, Topo I)
📌 Functional Importance:
chatgpt
DNA Compaction: Essential for fitting the chromosome inside the cell.
Gene Expression Regulation: DNA supercoiling affects promoter accessibility.
Replication & Segregation: Loop domains allow localized control of DNA activities.
Environmental Response: Changes in supercoiling help bacteria respond to stress (e.g., heat shock or antibiotics).
📌 Final Integration Line
chatgpt
Bacterial chromosome organisation is a multi-level strategy that balances compaction, accessibility, and flexibility, allowing the genome to be stored efficiently while remaining dynamically regulated in response to the cell’s needs.
what drives the structure of DNA
- Base stacking
- Stacking energy between alternative bases
o Electron orbitals
o Responsible for stability - Stack at slight angle
o Angle depends on nature of base
o Stack so they are at optimal distance apart
o Creates a twist
Genomes sizes;
- Some organisms have big genomes and some have small
- Size is not proportional to complexity
Bacterial genome sizes:
- Can relate genome size to:
o Lifestyle (generalists vs. specialists)
o Complexity of environment
o Differentiation - Genome size reflects gene content
o Density tends to be higher (for all bacteria)
o Gene rich (1 gene per 1kb)
o Operons
Bacteria are economically good at using their DNA -> get a lot out of it
bacterial chromosomes can be…
circular or linear
e.g.
e coli circular
streptomyces linear
borrelia linear (DNA loops at end)
bacteria can have…
Multiple chromosomes
- Many bacteria have more than one chromosome
e.g. rhodobacter sphaeroides
packaging of bacterial chromosomes
How do you pack mm worth of DNA into a bacteria
- The DNA Is condensed
- No nuclear membrane
- Some force in bacterial cytoplasm causing DNA to cluster
packaging of bacterial chromosomes:
nucleoid
- Packaged by 3 different mechanisms
o Molecular crowding
o Proteins and RNA
o Supercoiling
packaging of bacterial chromosomes:
nucleoid
molecular crowding
- High concentration of macromolecules leads to entropy driven compaction f the DNA
- The cytoplasm of E. coli contains approx. 300-400 mg/ml of macromolecules
o Very high concentration! - “Making condensates and creating phase”
- Phase separation
- Water dissolved in biomolecule
o Take any biomolecule in to high conc will flip into a phase
Phase is the organic molecules
water as guest
o Often when molecules in phase don’t have a regular structure
packaging of bacterial chromosomes:
nucleoid
proteins and RNA
- Experimental findings
o Isolated nucleoids
1) cells treated with lysozyme and Brij58 (non-ionic detergent – mild conditions)
2) loaded and spun on sucrose gradient at high speed
o Compact structure -> supercoiling
o Destroyed by proteases or RNases
o DNA/protein/RNA - Found that need RNA and protein to hold it together
- Bacteria contain proteins that hold the DNA together
—> NUCLEOID-ASSOCIATED PROTEINS (NAPs)
packaging of bacterial chromosomes:
nucleoid
proteins and RNA: NAPs
Present in high concentrations (unlike transcription proteins)
Binds promiscuously – needs to work across whole sequence
packaging of bacterial chromosomes:
nucleoid
supercoiling: in watson crick structure
o 210 bp long
o 10.5 bp per twist
o 210/10.5 = 20
o Watson-krick is the lowest energy, any change will require energy to be pumped in
packaging of bacterial chromosomes:
nucleoid
supercoiling:
add more twists?
- Cannot just add more twists
o would be thermodynamically unstable
o DNA corrects itself
Positive supercoiling
packaging of bacterial chromosomes:
nucleoid
supercoiling:
take out twists?
o Also thermodynamically unstable
o DNA wants to snap back
Negative supercoiling
In our case (for this module) DNA always has negative supercoiling
packaging of bacterial chromosomes:
nucleoid
supercoiling:
negative supercoiling topoisomers
- two structures chemically identical
o Topoisomers
o Same atoms but different tompomology - Both have compensated for the less twists
- In the interest of the cell to have DNA that is compact via negative supercoiling
- As it gives entry into a complicated structure
packaging of bacterial chromosomes:
nucleoid
supercoiling:
global DNA topology
o DNA supercoiling is the winding of the DNA strands
DNA replication
Transcription
