Bacterial organelles and substructures- lecture 25

Question 1

How are magnetotaxis arranged in the bacteria?

Answer 1

They are lined up in the center of the cell.

Question 2

General organelle structure

Answer 2

• proteinaceous or membranous barriers keep it separate
• performs a specialized function at a specific sub cellular location
• sometimes factor must be partitioned from the rest of the cell to protect their function
• must be synthesized or expanded, must be segregated to daughter cells

Question 3

What is the general structure of the the bacterial nucleoid?

Answer 3

• highly compacted region on center of cell where DNA resides
• Not surrounded by a membrane or protein shell
  
  • > accessible to medium sized proteins
• Not permeable to large components like ribosomes
• serves an essential function in all bacteria- organizing in DNA in a compact yet accessible manner, and segregating it to daughter cells before cell division

Question 4

General bacterial chromosome structures

Answer 4

• most bacteria have a single, circular chromosome
• they are haploid (1n)- 1 instance of each gene
• before replication, we refer to the single genome as 1c, after replication, there are two identical copies

Question 5

Different bacteria and their ori/ter sites

Answer 5

Bacillus Subtillus(sporulating): ter sites facing inward, origin sites facing out.
- origin at poles
C. Crescentus: Ter site at one end, originally site at other
- origin replicated and moves to other pole
E.coli slow growth: Ori and term in center
E.Coli fast growth: occurs in rich media, high temp, multiform replication

Question 6

How do bacterial chromosomes replicate?

Answer 6

Replication begins at ori site and ends at term.
Replication can begin before its finished=> multifork replication
Multiple replication forks meet in the middle at the terminus

Question 7

Why is multiform replication beneficial

Answer 7

A cell can get a head start to make more DNA if it gets a head start-> can make more offspring-> complete cell cycle quicker

Question 8

How can we visualize DNA loci in bacteria?

Answer 8

LacI is the DNA binding protein-> binds at Lac O
Determine where cell genomic loci localize within a cell through fluorescent reporter operator system (FROS)
- uses site specific DNA binding proteins fused to fluorescent protein
- place array of binding sites near locus you want to investigate=> fluorescence coalesces into a focus at that site
- different DNA binding proteins/sites labeled with different colors can probe multiple sites

Question 9

What is transertion?

Answer 9

Genes encoding membrane proteins are transcribed, translated, and the polypeptide is inserted into the membrane at the same time

=> loops of DNA have to access the membrane of a bacterial cell

Question 10

How do bacterial cells increase nucleoid compaction>

Answer 10

The DNA supercoils

Question 11

How do transcription and translation affect DNA compaction?

Answer 11

Transcription causes DNA to condense, potentially through formation of supercoils or multiple RNAPs interacting with each other

Translation causes DNA to expand, likely because the ribosomes lie outside the nucleoid and the DNA must travel to the membrane for transertion

Question 12

What do Nuceloid associated proteins do?

Answer 12

Bind to DNA and help it compact/supercoil

more are found where more are needed, origin of replication

Question 13

What is the function of parABS

Answer 13

ParB is a DNA binding protein that binds to origin proximal sites called parS sites
-> parB proteins spread out along the DNA near the parS site, condensing it and recurring SMC proteins

Question 14

What is the SMC complex?

Answer 14

• encircles double helix
• stands for Structural maintenance of Chromosomes, is a ring shaped protein complex that is thought to encircle the DNA double helix
• analogous proteins are found in all domains of life (in eukaryotes-cohesin and condensin)

Question 15

How to segregate replicated chromosomes

Answer 15

SMC replication rings are loaded at origin and slide down DNA, surpassing protein complex and transcription/translational things

Purpose: Compact and resolve newly replicated chromosomes

ParA and parB push/pull chromosomes apart

Question 16

What proteins/actions are involved in segregating the replicated chromosomes?

Answer 16

To separate the strands, they need to be unlined. When they are replicated they either make a continuous chromosome dimer or a two-chromosome linked chromosome concatenation.

Topoisomerase(gyros and topoIV) cut and twist DNA to relax it, but they don’t always complete the job and the chromosomes end up linked

Homologous recombination between the chromosomes van turn them into a single chromosome.

Question 17

How and when are linked chromosomes resolved?

Answer 17

Linked chromosomes are separated by the closing of the septum.

FtsK is a DNA-pumping machine that pumps DNA out towards terminus, it activated TopoIV to resolve concatenated DNA then FtsK activates recombinases XerC and XerD to resolve dimers.

Question 18

Organelles that store nutrients.

Question 19

Iron storing granules

Answer 19

membrane bound iron storage compartments
assembly controlled by fez genes, expression of fez in E.coli led to ferrosome formation

ferrosome membrane contains Iro-pumping channel called FezB that helps accumulate Fe2+

Question 20

organelles functioning in locomotion/taxis

Answer 20

Gas vesicles and magnetosomes
magnetosomes have magnetite or reignite that form linear chains, enable magnetotaxis-locomotion oriented along the earths magnetic field
-magnetite is deposited inside the magnetosome, expand as mineral gets bigger

mam genes are responsible for magnetosome biosynthesis, 35 mam genes are sufficient to form magnetosomes

Actin homolog mamK forms a filament that organizes magentosomes into a chain, mamK is required to evenly segregate magentoseomes into daughter cells

Question 21

organelles that function in metabolism

Answer 21

Carboxysomes have protein shells that contain carbon fixation machines and trap CO2

Annamoxosomes are membrane bound organelles where anaerobic oxidation of ammonia takes place

Thylakoids are membranous intercellular structures where light driven photosynthesis reactions occur

Concentrating metabolic enzymes and metabolites enhances the efficiency of these processes

Question 22

Caboxysome

Answer 22

Surrounded by a protein shell impermeable to CO2 and O2, but bicarb can be diffused in and converted to CO2 by carbonic anhydrase
-> We want O2 out because ut competitively binds to Rubisco

ParA like protein McdA oscillates along nucleoid, carboxysomes bind McdA for even distribution

Question 23

Organelles that serve to isolate/protect their contents

Answer 23

• Jumbophage nucleus: large genomes, very complex, form protective shell

During infection, phage genome does not have to be segregated because the cell will lyse before division

Proteinaceous shell encapsulates the phage DNA, phage RNA is transcribed inside
=> separate transcription and translation

Allows to evade DNA targeting defenses like restriction endonuclease and CRISPR