Lecture 2 (AT) Flashcards
(15 cards)
Describe the general structure of a bacterial origin.
7 strong gene cluster, with OriC found between DnaN and DnaA.
There are several differences in OriC across bacteria. Name some of these.
- Number and spacing of DnaA boxes.
- Location of DnaA boxes.
- The length of OriC.
- Can be continuous or bipartite (DnaA boxes found in different intergenic regions).
Describe replication initiation in bacteria.
- DnaA binds DnaA boxes. Link together and oligomerise.
- DUE unwinds.
- DnaC recruited, this loads DnaB.
- DnaB unzips the rest of the genome.
- Primase (DnaG) and clamp (DnaN) are recruited.
What is the main point of DNA replication regulation in bacteria? What is mainly responsible for this regulation?
INITIATION. Regulated by DnaA, which has three forms: DnaA, DnaA-ATP (active form), DnaA-ADP.
How does the protein Hda negatively regulate initiation? Mention RIDA.
Hda protein binds to DnaA and DnaN. This 3 protein complex then converts DnaA-ATP –> DnaA-ADP. This process is called RIDA, and is regulatory as it can only occur when DnaN is present.
What does RIDA stand for?
Regulatory Inactivation of DnaA.
Transcription of DnaA is a major part of initiation regulation and is itself auto-regulated. Explain this.
- The DnaA promoter also contains DnaA boxes.
- Once the DnaA protein is transcribed and translated it becomes involved in replication.
- Once used in replication it loses its ATP: becomes DnaA-ADP.
- Can then bind to promoters of its own gene and suppress its production.
- DnaA-ATP is a stronger repressor.
- When either are present DnaA repression will occur to control levels in the cell.
Hemi-methylation negatively regulates replication initiation. Explain this.
When DNA is replicated, the new origins are hemi-methylated = parental strands are methylated whilst the newly synthesised strands are not. SeqA binds to the new strands immediately after replication initiation to prevent immediate DnaA oligomerisation and re-initiation. Remains bound for 1/3 of the cell cycle. Will eventually dissociate and dam methyltransferase will methylate the A’s and C’s of the origin.
What does IHF (protein) stand for?
Integration Host Factor.
How does IHF positively regulate initiation?
It is a sequence-specific DNA binding protein that bends the DNA, bringing DnaA boxes closer together and promoting the formation of oligomers.
How does datA negatively regulate initiation?
Contains several DnaA boxes. DnaA protein can bind here instead of OriC.
How do DARS1 and DARS2 positively regulate initiation?
They promote the conversion of DnaA-ADP –> DnaA-ATP.
Breifly explain cell division in terms of the Z ring and septal cell wall formation.
The Z ring is the division machinery that assembles from the protein Ftsz in the middle of the cell. Must occur between the segregated chromsomes. Once assembled, the divisome is formed through recruiting more division proteins. Begins to synthesise septal peptidoglycan.
Explain the term ‘filamentation’.
This occurs when cell division and replication goes wrong. Performed in rod shaped cells –> they keep replicating but don’t divide, and so form long filaments. This is potentially a stress response and a potential survival strategy (takes longer for immune cells to uptake the larger cells).
Explain the term ‘endoreplication’.
This is the homolog of filamentation in eukaryotes. The cells skip mitosis and do not divide.
