Processes

Divisome Complex

FtsZ: tubulin homolog protein, polymerizes into ring structure called Z-ring at division site (determines cell diameter, manages growth, recruits proteins)

FtsN: triggers/stabilizes divisome assembly: Z ring to septal wall synthesis

PBP3: penicillin binding protein, crosslinks new PG strands to build septal cell wall

PBP1: assists in PG synthesis/remodeling at division site

Bacterial Cytoskeletal Proteins

FtsZ - forms circumferential ring at division septum

MreB - helps coordinate PG synthesis, needed for rod bacteria

CreS (crescentin) - forms polymer on inner side of crescent-shaped bacterium. one edge only, prevents cell wall growth so cell bends into crescent

Min System

Ensures ZRing assembles at correct place and cells evenly divided

MinC - directly inhibits FtsZ polymerization

MinD - ATPase that recruits MinC to membrane, helps drive oscillation

MinE - forms ring chasing Min D and MinC from pole to pole

Steps of Min System

1.) MinD-ATP/MinC bind to cell membrane

2.) more MinD cooperatively recruited

3.) GFP signaling increased at one pole

4.) MinE binds MinD-ATP/MinC, causing ATP → ADP hydrolysis

5.) MinD-ATP/MinC falls off membrane

6.) MinD exchanges ADP for ATP incytoplasm

7.) MinD-ATP and MinC bind a opposite pole

8.) MinD-ATP signal increases at new pole as it fades at other

MinD mostly removed from first patch

10.) MinE relocates to new patch

Nucleoid Occlusion

ensures Z-ring not formed over nicleoid/DNA so unsegragated DNA is not divided

1.) SimA/Noc binds to specific DNA sequences distributed across chromosome (these sequences absent at ter area where Z ring forms)

2.) When bound to DNA, proteins ihibit FtsZ polymerization in that vicinity (ensures Z ring doesnt form over nucleoid)

Positive Supercoils

overwind DNA, less bp’s per turn

seen in archaea at high temps

Negative Supercoils

Underwind DNA, more bp’s per turn

seen in archaea, eukaryotes, and prokaryotes

DNA packs smaller

helps unwind DNA during replication/translation

Type 1 Topoisomerases

single subunit enzymees

cleave and reseal 1 DNA strand

relieves stress from negative supercoils

Type 2 Topoisomerases

multi subunit enzymes

cleave both DNA strands and use ATP hydrolysis to change supercoiling

DNA gyrase: can relieve supercoilsor introduce negative supercoils to relax

1.) GyrA grabs one section of dsDNA, creates coil

2.) GyrA introduces dsbreak and holds two ends apart

3.) GyrB ATPase passes intact ds section through dsbreak

4.) GyrA rejoins cleaved DNA and opens at other end, allowing strand that has passed to exit

Replication Initiation

1.) DnaA accumulates during cell growth. DnaA-ATP proteins bind repeated 9mer sequence in oriC.

2.) Binding of DnaA causes strand separation of 13mer repeats

3.) DNA helicase loaders (dnaC) open DNA helicase (dnaB) ring and place it around ssDNA. Loading of helicase triggers release of helicase loader

4.) Helicase recruits DNA primase (dnaG) to make primers. Clamp loaders carrying two DNA Pol 3 enzymes load a sliding clamp at each primer. Simultaneously, helicase-primase unwinds DNA and synthesizes lagging strand primers

5.) One DNA pol binds clamp. leading strandy synthesis begins at primer. new clamp added to lagging strand, recruiting more DNA pol

Replication Elongation

1.) leading strand DNA Pol 3 replicates ls. DNA helicase remains on lagging strand, unwinding dsDNA moving into replisome

2.) lagging strand DNA pol synthesizes lagging strand, which loops out after passing through the pol

3.) After helicase has gone ~1000 bp’s, another RNA primer is synthesized on each lagging strand

4.) lagging strand pol bumps 5’ end of previous fragment → pol is released and clamp disengaged

5.) New clamp assembled on newly primed lagging strand

6.) DNA pol binds clamp and begins synthesizing another Okazaki fragment

Removal of RNA Primers

Pol 1 or RNase H cleves RNA

DNA Pol 1 fills gap using 3’OH end of DNA fragment

ligase repairs phosphodiester nick

• ligase uses NAD+ as substrate

• provides energy to create phosphodiester bond

• phosphorous droves reaction of O- attacking OH

Ending Replication → Tus/Ter

Tus binds Ter to end replication

act together to trap forks

Ending Replication → Topoisomerase IV

separates ringed catenanes formed at completion of replication

cuts one DNA duplex and threads other through break, resolving catenane

handles most catenanes

Ending Replication → XerC and XerD Resolvases

XerC (first): cuts one strand on each daughter chromosome and pairs at dif sites. swaps nicked ends and ligates, forming Holliday junction

XerD (second): catalyzes 2nd pair of strand exchanges, fully separating daughter chromosomes

Theta Replication (Plasmids)

two forks, works both ways, does both strands at same time. uses DNA pol 3, helicase, and primase

1.) dsDNA unwinds at replication origin

2.) this produces ssDNA templates for synthesis. replication bubble forms with a rep fork at each end

3.) Forks proceed around circle

4.) eventually 2 circular DNA molecules are made

Rolling Circle Replication (plasmids)

2 step process w/ 1 replication origin, no need for dnaG (primase)

+ Strand Synthesis (first)

1. Rep A forms dimer, nicks + strand

2. DNA Pol 3 synthesizes new + strand

3. RepA cleaves old + strand and ligates ends to form circle

- Strand Synthesis (second)

1. RNA pol lays primer

2. DNA pol 3 synthesizes new - strand

3. DNA pol 1 removes RNA primer/fills in gaps

4. Ligase seals nick

Plasmid Partitioning

ensures each cell gets 1 plasmid

1. Filament extends on plasmid as added ParM monomer hydrolyzes ATP

2. Plasmids diffuse around the cell

3. Filaments connect two plasmids

4. Stable filaments polymerize to drive plasmids toward opposite poles

5. Plasmid hitting cell pole triggers filament detachment and depolymerization