7.1 - Chromosome Organization Flashcards
What is the shape of a typical bacterial chromosome?
Circular
Are all bacterial chromosomes circular? Give examples
No some are linear for example:
Borrelia burgdorferi which causes lime disease
Do bacteria only have circular or linear chromsomes?
No some can have both such as Agrobacterium tumefaciens
Which species have the largest genome amongst bacteria?
Streptomyces
When does a plasmid become a chromsome?
The moment when, if lost, the bacteria cannot survive without it
How much of the human genome is coding for genes?
Less than 1%.
There are a lot of repetitive sequences like transposons and introns (spliced out of mRNA).
How much of the bacterial genome is coding DNA
90%.
Introns and repetitive elements are rare in bacteria
What is the most common repeptitive element in bacteria?
The IS (insertion sequence) element which are mobile elements
What does it mean when we say an RNA is monocistronic. What organism has monocistronic RNA?
When 1 mature mRNA makes 1 protein. Eukaryotes have this property
What does it mean when we say an RNA is polycistronic. What organism has polycistronic RNA?
When 1 mature mRNA makes multiple proteins. Eubacteria and archaebacteria have this property
What regulatory system do most bacteria have?
Operons
What is an operon?
A cluster of genes under the control of one promoter. Those genes are often involved in the same metabolic process.
What is a regulon?
A gene whose transcription results in the production of a regulatory protein that regulates the expression of promoter elements
What is the accepted bacterial nomenclature
lacZ = gene LacZ = protein
Any number after the “Z” designates an allele of the gene, or a mutant.
What are nucleoids?
Bacterial chromsomes are compacted into nucleoids.
What is DAPI
A chemical dye that has an affinity to DNA
What happens when bacterial cells are treated with DAPI?
When some bacteria are treated with DAPI, we observe a blue stain at a specific location of the cell. This means that the bacterial cell has a nucleoid that is contained in a specific location/compartment in the cell. When all the cell is stained, this means that there is no nucleoid and the DNA is floating in the whole cytoplasm.
What is a significant difference between bacteria and eukaryotes and archae
Bacteria, unlike the other two, do not have histones or nuclear membranes.
How is DNA compacted in the nucleoid?
DNA is compacted by histone-like anchoring proteins, as well as by supercoiling/twisting to form loops. When histone-like proteins try to twist the DNA, the DNA will respond by trying to untwist itself. Since the DNA can’t untwist itself, it will release the tension due to the twisting by forming what we call a negative supercoil. A nick in a single strand will result in relaxing the supercoiling in the nicked strand. Most bacterial genomes are organized in negative supercoils.
How is negative supercoiling maintained?
With Topoisomerase I and II
What does Topoisomerase do?
Topoisomerase acts to regulate DNA supercoiling by catalyzing the winding and unwinding of DNA strands.
What is the general mode of action of topoisomerases?
o They cut the DNA backbone.
o They pass the DNA strands through one another to coil or relax.
o They ligate the DNA backbone
How does Type I topoisomerase work?
They work by breaking one strand of DNA, twisting the DNA to pass it through the gap and then re-ligating it.
How does Type II topoisomerase work?
They work by breaking both strands of DNA (needs ATP), twisting them and then re-ligating them. (DNA gyrase most typical type II)
Why are bacterial topoisomerases targets for antibiotics?
Because eukaryotic and bacterial topoisomerases are different
What is the procedure for Type I Topoisomerase?
(1) Type I topoisomerase will cleave 1 strand of a double helix and hold on to both ends of the break.
(2) It then passes the intact strand through the break.
(3) Then it re-ligates the strand.
(4) Depending on where the intact strand is passed (to the left or to the right) this mechanism can either lead to the addition of 1 negative supercoil or the release of 1 negative supercoil.
True or false? All organisms have type II topoisomerases?
True
What is the major type of type II topoisomerase in E.coli?
DNA gyrase.
It uses ATP to wind and unwind DNA (ATP drives unwinding).
How many subunits does DNA gyrase have?
2: GyrA and GyrB
How does DNA gyrase work?
(1) GyrB will grab one section of the dsDNA.
(2) GyrA will then use the energy of ATP hydrolysis to introduce a double-stranded break in the DNA section grabbed by GyrB. GyrA will hold the 2 ends of the break apart by covalently binding to them (transient bond).
(3) GyrA ATPase will then pass the intact double-stranded section through the double-stranded break.
(4) GyrB will re-join the cleaved DNA and opens at the other end, allowing the strand that has passed through to exit.
(5) This allows the supercoiling of DNA.
What is reverse DNA gyrase?
Archaea thermophiles possess an unusual gyrase called reverse DNA gyrase, which introduces positive supercoils into the chromosome in order to protect the DNA from thermal denaturation.
What is unique about eukaryotic topoisomerases?
They do not hydrolyze ATP
What kind of antibiotics bind DNA gyrase?
Quinolones
What step does Quinolones inhibit?
By binding to bacterial DNA gyrase, Quinolones inhibit the ligation step and thus prevents DNA replication but, more significantly, damage DNA.This will leave the DNA with a double stranded break bound to gyrase. Since GyrA is covalently bound to the ends.
What is the difference between quinolones and penicillin?
Quinolones disrupt DNA replication, whereas penicillin disrupts cell wall synthesis
What are the functions of gyrase in a cell?
(1) Maintains (-) supercoiling and compaction (bacterial DNA tension).
(2) Relaxes strain after replication fork by unwinding the strands.
o Gyrase will cleave the DNA molecule upstream, allowing the unwinding to take place so that the tension created by the moving replication fork is reduced.
(3) Helps chromosome separation by performing several breaking and joining reactions.
What is Topo IV?
Although gyrase is able to separate chromosomes, it does so very poorly. Another protein called Topo IV separates chromosomes much better. Topo IV is a gyrase paralog, meaning that both proteins were derived from an ancestral gene
What is homologous recombination?
The exchange of DNA sequences between 2 similar or identical DNA molecules.
What happens after homologous recombination in linear chromosomes?
There is no problem to separate the recombinant DNA molecules.
What happens after homologous recombination in circular chromsomes?
The chromosomes cannot separate. Homologous recombination therefore causes problems for circular chromosomes: recombination would result in 1 big chromosome.
What is XerCD site specific recombination?
Protein XerCD will separate this big chromosome by performing cuts and then ligating at specific sites on the chromosome called “cer sequence”
What happens when there is a mutation in XerCD?
Mutations in XerCD will lead to cells failing to separate their chromosomes so the bacterium will not divide properly.
What structures have XerCD site-specific recombination sequence called cer sequences?
All circular bacterial chromsomes and large plasmids
