RECOMBINATION:
Recombination is a process that brings about reassortment of genetic information in and
among chromosomes. Recombination serves several functions in organisms, including
DNA repair in bacteria and eukaryotes, and ensures the correct alignment and segregation of
chromosomes during meiosis in eukaryotes.
However, bacteria have found ways to increase their genetic diversity through three
recombination techniques: transduction, transformation and conjugation.
1. Combination of favourable alleles
two members of a species, each of which acquires a different mutation, without
recombination, the combination of the two favourable mutations in a single progeny of these
individuals will depend on further mutation (would be very slow) with recombination this
outcome arises rapidly owing to genetic exchange
2. Avoidance of deleterious alleles (alleles that can confer a disadvantage to a particular
organism)
All organisms carry a burden of deleterious alleles caused by mutation; there are 2 ways of
avoiding accumulation of these alleles:
1.back-mutation (very slow)
2. Recombination between individuals carrying different deleterious regions, to regenerate
progeny lacking them (more rapid)
Without recombination a species has no escape from the continuous accumulation of
deleterious alleles
Recombination can be broadly divided into:
1. Homologous – like sequence recombines with like sequence
2. Non-homologous – sequence that recombine have no relation to each other at all
Instances in nature when we see it:
1. During bacterial conjugation (homologous recombination) – mechanism by which
antibiotic resistance spreads throughout the population of the same bacteria
There are strains of bacteria referred to as high frequency recombination bacteria because
they contain a copy of the F plasmid which is integrated into its genome; the F plasmid can
make a copy of itself and it can stop dragging itself into another bacterium through a
conjugation tube and as it drags itself into another bacterium it drags copies of the genome
that it was part of
2. Site specific recombination - recombination of the genome of a bacteriophage
bacteriophage is a virus that infects bacteria ; the genome of the bacteriophage can
recombine into the genome of the host bacterium
Another example of homologous recombination – occurring between DNA molecules with
very short sequences in common
Bacteriophage λ:
Lytic pathway - the genome of the bacteriophage can enter a bacterium and then it
repurposes the capacity of the bacterium to synthesize things in order to transcribe its
genome and make more viral particles; effectively the genome of the lambda phage is
, convincing the bacterium to become a factory for production of more phages and this is
immediate viral replication- the genome is replicated, the proteins involved in encapsulating
the phage as well and the host bacterium is killed within 20 minutes; when there is no more
bacterium the replication stops and the bacteriophages stay as a constant number; lytic
phase does not involve recombination the lysogenic pathway does
Lysogenic pathway- the bacteriophage injects its genome into bacterium; homologoes
recombination; the lambda genome is incorporated into bacterial genome; every time the
bacterium replicates its genome it also replicates the lambda genome; when the bacteria
reach harsh condition, the lambda genome can make proteins that can detect the stress and
then the lambda genome gets out and then the cycle becomes lytic
3. Transposition (non-homologous recombination) - referring to the mobile genetic
elements found in all living organisms; these are areas of the genome that can jump into
other parts of the genome referred as jumping genes; if a piece of DNA is going to jump into
another part of the genome that has to happen by recombination
A. Replicative transposons - the original stays in place in the genome and it makes copy and
then this copy recombines into the genome and other locations
B. Conservative transposons - replicative phase is not involved but the original somehow
rips itself from the genome and jumps into another position of the genome
C. Retroelements – transpose via an RNA intermediates
All of these by definition involve nucleic acid recombining into another part of the genome
and therefore all of them involve non0homologous recombination.
4. DNA repair (homologous and non-homologous recombination) – all of the modes of
recombination originate from DNA repair – it is the first time in nature where recombination
happens
a. Non-homologous recombination
Double strand break (DSB) is a break at equivalent position in a double helix both
phosphodiester linkages are gone; many DNA damage but the DSB is the most toxic one
and leads to the appearance of many mutations in the genome and the accumulation of
the mutations in the genome is one of the things that lead to developing tumors; can be
caused by ionizing radiation from the outside or by things going wrong inside either way
this happens per cell per day; as soon as the breakage happens the cell must prevent the
two ends of the chromosomes drifting apart from each other, so they are kept in close
proximity to each other by the binding of Ku proteins – they bind to the free ends of the
DNA that have been liberated by the break, thus the ends of the chromosomes are not
allowed to drift apart from each other and this gives the cell the opportunity to repair
the damage; does that by recruiting a signaling pathway involving a DNA depending
protein kinase which recruits a protein called XRCC4 which recruits a DNA ligase which
has the key role by replacing the phosphodiester bond that is missing; non-homologous
because the recombining sequences are not related to each other
b. Homologous recombination
In order that to happen, the damage chromosome has to recombine with the
undamaged version of the chromosome because the undamaged one is going to be used
as a template for repairing the damaged one; this means that mode of replication can
Recombination is a process that brings about reassortment of genetic information in and
among chromosomes. Recombination serves several functions in organisms, including
DNA repair in bacteria and eukaryotes, and ensures the correct alignment and segregation of
chromosomes during meiosis in eukaryotes.
However, bacteria have found ways to increase their genetic diversity through three
recombination techniques: transduction, transformation and conjugation.
1. Combination of favourable alleles
two members of a species, each of which acquires a different mutation, without
recombination, the combination of the two favourable mutations in a single progeny of these
individuals will depend on further mutation (would be very slow) with recombination this
outcome arises rapidly owing to genetic exchange
2. Avoidance of deleterious alleles (alleles that can confer a disadvantage to a particular
organism)
All organisms carry a burden of deleterious alleles caused by mutation; there are 2 ways of
avoiding accumulation of these alleles:
1.back-mutation (very slow)
2. Recombination between individuals carrying different deleterious regions, to regenerate
progeny lacking them (more rapid)
Without recombination a species has no escape from the continuous accumulation of
deleterious alleles
Recombination can be broadly divided into:
1. Homologous – like sequence recombines with like sequence
2. Non-homologous – sequence that recombine have no relation to each other at all
Instances in nature when we see it:
1. During bacterial conjugation (homologous recombination) – mechanism by which
antibiotic resistance spreads throughout the population of the same bacteria
There are strains of bacteria referred to as high frequency recombination bacteria because
they contain a copy of the F plasmid which is integrated into its genome; the F plasmid can
make a copy of itself and it can stop dragging itself into another bacterium through a
conjugation tube and as it drags itself into another bacterium it drags copies of the genome
that it was part of
2. Site specific recombination - recombination of the genome of a bacteriophage
bacteriophage is a virus that infects bacteria ; the genome of the bacteriophage can
recombine into the genome of the host bacterium
Another example of homologous recombination – occurring between DNA molecules with
very short sequences in common
Bacteriophage λ:
Lytic pathway - the genome of the bacteriophage can enter a bacterium and then it
repurposes the capacity of the bacterium to synthesize things in order to transcribe its
genome and make more viral particles; effectively the genome of the lambda phage is
, convincing the bacterium to become a factory for production of more phages and this is
immediate viral replication- the genome is replicated, the proteins involved in encapsulating
the phage as well and the host bacterium is killed within 20 minutes; when there is no more
bacterium the replication stops and the bacteriophages stay as a constant number; lytic
phase does not involve recombination the lysogenic pathway does
Lysogenic pathway- the bacteriophage injects its genome into bacterium; homologoes
recombination; the lambda genome is incorporated into bacterial genome; every time the
bacterium replicates its genome it also replicates the lambda genome; when the bacteria
reach harsh condition, the lambda genome can make proteins that can detect the stress and
then the lambda genome gets out and then the cycle becomes lytic
3. Transposition (non-homologous recombination) - referring to the mobile genetic
elements found in all living organisms; these are areas of the genome that can jump into
other parts of the genome referred as jumping genes; if a piece of DNA is going to jump into
another part of the genome that has to happen by recombination
A. Replicative transposons - the original stays in place in the genome and it makes copy and
then this copy recombines into the genome and other locations
B. Conservative transposons - replicative phase is not involved but the original somehow
rips itself from the genome and jumps into another position of the genome
C. Retroelements – transpose via an RNA intermediates
All of these by definition involve nucleic acid recombining into another part of the genome
and therefore all of them involve non0homologous recombination.
4. DNA repair (homologous and non-homologous recombination) – all of the modes of
recombination originate from DNA repair – it is the first time in nature where recombination
happens
a. Non-homologous recombination
Double strand break (DSB) is a break at equivalent position in a double helix both
phosphodiester linkages are gone; many DNA damage but the DSB is the most toxic one
and leads to the appearance of many mutations in the genome and the accumulation of
the mutations in the genome is one of the things that lead to developing tumors; can be
caused by ionizing radiation from the outside or by things going wrong inside either way
this happens per cell per day; as soon as the breakage happens the cell must prevent the
two ends of the chromosomes drifting apart from each other, so they are kept in close
proximity to each other by the binding of Ku proteins – they bind to the free ends of the
DNA that have been liberated by the break, thus the ends of the chromosomes are not
allowed to drift apart from each other and this gives the cell the opportunity to repair
the damage; does that by recruiting a signaling pathway involving a DNA depending
protein kinase which recruits a protein called XRCC4 which recruits a DNA ligase which
has the key role by replacing the phosphodiester bond that is missing; non-homologous
because the recombining sequences are not related to each other
b. Homologous recombination
In order that to happen, the damage chromosome has to recombine with the
undamaged version of the chromosome because the undamaged one is going to be used
as a template for repairing the damaged one; this means that mode of replication can
