Mobile Genetic Elements

Mobile Genetic Elements

Lecture 11: Expected Learning Outcome (ELO)

1. What are mobile genetic elements
2. Concept of accessory genetic materials, plasmids, episomes
3. Consequence of acquiring accessory genetic materials
4. Integrative and nonintegrative plasmids
 Mobile Genetic Elements
Examples of mobile genetic elements

Plasmids

Phage genomes (prophage, episome)

Genomic islands

Insertion sequence elements

 Accessory Genetic Elements

Plasmids
A plasmid is a small DNA molecule that is
physically separate from, and can replicate
independently of, chromosomal DNA within a
cell.

The term plasmid was first introduced by

the American molecular biologist Joshua
Lederberg in 1952.
Plasmids can confer resistance to one or
more antibiotics
Plasmids must have their own origin of
replication, and hence capable of replicating
independent of the bacterial chromosome
Some Key Terms

plasmid: A circle of double-stranded DNA that is

separate from the chromosomes, which is found
in bacteria and some protozoa.

mobilome: The entirety of the mobile

(transposable) elements of a genome.

replicon: a region of DNA or RNA, that replicates

from a single origin of replication.
Functions of Plasmids
Plasmids usually occur naturally in bacteria, but are
sometimes found in archaea, and even in eukaryotic
organisms (e.g., in Saccharomyces cerevisiae).

Plasmids provide a mechanism for horizontal gene transfer

within a population of microbes and typically provide a
selective advantage under a given environmental state.
Plasmids may carry genes that provide resistance to
naturally occurring antibiotics in a competitive
environmental niche, or the proteins produced may act as
toxins under similar circumstances.

Plasmids can also provide bacteria with the ability to fix

elemental nitrogen or to degrade certain organic matter
that provide an advantage when nutrients are scarce.
There are two types of plasmid: Non-integrating plasmids replicate
as with the top instance, whereas episomes, the lower example,
can integrate into the host chromosome or also replicate
independently of the host chromosome
Plasmid sizes vary from 1 to over 1,000 kbp. The
number of copies of identical plasmids in a single
cell can range anywhere from one to thousand
copies under some circumstances. Plasmids can
be considered part of the mobilome because
they are often associated with conjugation, a
mechanism of horizontal gene transfer.

Plasmids provide a mechanism for horizontal

gene transfer within a population of microbes
and typically provide a selective advantage under
a given environmental state. Unlike viruses, they
are naked DNA and do not encode genes needed
to encase the genetic material (e.g., Capsid).
Incompatibility Groups
It is possible for plasmids of different types to
coexist in a single cell. Several different plasmids
have been found in E. coli.

However, related plasmids are often

incompatible, in the sense that only one of them
survives in the cell population, due to the
regulation of vital plasmid functions.

Thus, plasmids can be assigned into

incompatibility groups.
Plasmids must regulate their copy number (average
number of plasmid copies per cell) to ensure that
they do not excessively burden the host or become
lost during cell division. Plasmids may be either high
copy number plasmids or low copy number plasmids;
the regulation mechanisms between these two types
are often significantly different.

High copy number plasmids, also called relaxed

plasmids, require a system to ensure that replication
is inhibited once the number of plasmids in the cell
reaches a certain threshold.

Low copy number plasmids, also called stringent

plasmids, require tighter control of replication.
Plasmid incompatibility is usually defined as the failure
of two co-resident plasmids to be stably inherited
together in the absence of external selection. In simpler
terms, if the introduction of a second plasmid negatively
effects the inheritance of the first, the two are
considered to be incompatible.

Plasmids can be seen as selfish entities in evolutionary

terms. Having gained territory in a bacterial cell, they will
try to prevent any other plasmid co-residing with them.

Plasmid incompatibility is a very effective strategy for

protecting territory of a plasmid type within the bacterial
population.
The number of plasmids in a cell is governed by elements
encoded within the origin of replication (ori). It is not
possible to maintain two different type of plasmids that use
the same mechanism for replication in a single cell.
Therefore, plasmids fall into compatibility groups base on
their replication strategy and you cannot grow or use two
plasmids in the same cell system if the plasmids belong to
the same compatibility group.
What Makes Plasmids Incompatible with Each Other?

Competition for Replication Factors

It is widely accepted that competition for replication
factors leads to competition between plasmids.
Plasmids with inherent growth advantages such as
faster replication (due to their smaller size) or less
toxicity have the potential to rapidly outgrow other
plasmids in the cell. This is even more likely to occur
when the plasmid copy number is low. Taking into
account the number of cell division cycles occurring in a
single overnight culture, even small differences in
competitive advantage are thought to be able to lead to
rapid dominance of a culture by a single plasmid.
Plasmid incompatibility is intrinsically linked with copy number.
When a cell contains two incompatible plasmids, the cell cannot
distinguish between the origins of replication initiation. The result is
that replication is postponed until after the two plasmids have been
distributed to different cells
 Mechanism of incompatibility
Plasmids can be incompatible if they share the
same replication control mechanism. Under
these circumstances, both plasmids contribute
to the total copy number and are regulated
together. They are not recognized as distinct
plasmids. As such, it becomes much more likely
that one of the plasmids may be out-copied by
the other and lost during cell division (the cell is
"cured" of the plasmid). This is particularly
likely with low copy number plasmids. Plasmids
can also be incompatible due to shared
partitioning systems.
 Mechanism of incompatibility
A plasmid partition system is a mechanism that ensures
the stable inheritance of plasmids during bacterial cell
division. Each plasmid has its independent replication
system which controls the number of copies of the
plasmid in a cell. The higher the copy number is, the
more likely the two daughter cells will contain the
plasmid. However, high-copy number plasmids have a
cost for the hosting cell. This metabolic burden is lower
for low-copy plasmids, but those have a higher
probability of plasmid loss after a few generations.
Five main classes of plasmids according to function:
Resistance plasmids- contain genes that provide
resistance against antibiotics or poisons. They were
historically known as R-factors, also called R-plasmids
Col plasmids- contain genes that code for bacteriocins,
proteins that can kill other bacteria. Bacteriocins
produced by E. coli are called colicins, and hence the
name Col plasmids
Degradative plasmids- which enable the digestion of
unusual substances, e.g. toluene and salicylic acid.
Virulence plasmids- turn the bacterium into a pathogen
Fertility F-plasmids- (contain tra genes) are capable of
expression of conjugative pilli and transferring genetic
segments by conjugation to neighboring cells.