NAME : NOLUBABALO

SURNAME : NKOSAYIDLI

STUDENT NUMBER : 202108442

MODULE : MIC 222 ASSIGNMENT 2

TITTLE : INTRODUCTION TO MICROBIAL GENETICS

AND GENETIC RECOMBINATION.

DUE DATE : 19 OCTOBER 2022

QUESTION 1:

Transposable elements are the genomic parasites that are found in all genomes and
some of which displays sequence to certain viruses. Transposable elements are
specific sequence of DNA that codes for enzymes for their transposition from one
position to another position in the chromosome. Transposable elements undergoes
both replication and recombination process. However, they lack the site for origin of
replication. So, they must depend upon host DNA or plasmid for their replication. All
transposable elements are commonly known as transposons or mobile gene or
jumping genes that changes their location and insert into different location in a
chromosome or into other chromosome. Transposable elements contribute to the
repetitive sequences in the genome of the organisms. Both prokaryotic and
eukaryotic organisms such as bacteria, fungi, plants, animals as well as humans
have transposable elements in their genome, and they have their significant
structure and functional value. The transposable elements are broadly classified as
Insertion sequences (IS) and transposons. Insertion sequences are the simplest type
of transposable element with short sequences of about 1000 base pairs that is
present in Bacteria.

The horizontal transposon transfer which is common in all representatives of living

organisms is accompanied by their variability required for the acquisition of new
adaptive traits. During evolution the mechanisms of protection against viruses and
transposons, including RNA interference, DNA methylation, and histone modification,
began to be used to control the operation of the genomes which provides the
intercellular interactions this explains the emergence of multicellular organisms. For
eukaryotes, TEs gained importance in the transformation of genomes which
constitute a significant part of their genomes some viruses are most probably the
products of the evolution of TEs when they acquire the ability to transfer horizontally.
The diversity and distribution of viruses in eukaryotes indicates the significance of
TEs in their origin. Subsequently, viruses lose the traits of an evolutionary
relationship with their precursors due to their pronounced mutability. The distribution
and composition of TEs and viruses are specific for different domains of the living
which suggests their interconversions in evolution, in which TEs are sources of
viruses. Thus, DNA viruses constitute a larger portion in prokaryotes and DNA
transposons are also the most common TEs.  RNA viruses could emerge from retro-
TEs while DNA viruses could emerge from DNA-TEs. At the same time, the enzymes
used for integration in the host genome could acquire other properties required for
autonomous reproduction under the influence of several mutations. Both viruses and
TEs have an increased level of mutability. The endogenous retrovirus (ERV)
sequences are susceptible to disorganization by the formation of mutations with the
shift of the reading frame, stop codons, and deletions that affect their ability for
replication and transposition. The structural similarity of the hepatitis B virus with
retroviruses, as well as its ability to integrate into the host genome which also
suggests its origin from TEs. Viruses can act as TE vectors. The use of TEs for the
integration of viruses in the genome indicates both the possible origin of viruses from
TEs and the prospects of the use of this process in genetics.

FIFURE 1: Shows the structure of transposable elements.

Transposable elements are major components of eukaryotic genomes. However, the

extent of their impact on genome evolution, function, and disease remains a matter
of intense interrogation. Many transposable elements (TEs) use highly specific
mechanisms to direct their integration to sites in the host genome that lack coding
information. This minimizes the damage to the host genome that occurs during
integration Host. Many organisms have evolved various mechanisms to combat TE
activity. Examples include DNA methylation of TEs, small interfering RNA (siRNA)-
based degradation of TE mRNA and apolipoprotein B mRNA-editing enzyme -
mediated cytidine deamination of TE sequences. Viruses are a part of biology
because they possess genes, have group identity, replicate, evolve, and adapted to
hosts, biotic habitats, and ecological niches. Most viruses are persistent and
unapparent that is not pathogenic exogeneous retroviruses are distinct entities to
those species whose genomes into which they endogenize to become ERV and they
have an extracellular or virion stage with a protein capsid, ERVs are then also a part
of holobiont organism. Other TEs in a genome are not considered to be a part of
holobiont such as Transposable elements, as they seemingly can only transfer from
genome to genome and can have no independent existence like that of an
exogenous retroviruses’ species and some other exogenous RNA viruses that can
act in mutualism when endogenized in other genomes and their genomes are united
with the host genome into a holobiontic genome.

Figure 2: shows the structure of the virus.

Viruses cannot replicate on their own but rather depend on their host cells protein
synthesis pathways to reproduce. This usually occurs by the virus inserting its
genetic material in host cell co-opting the proteins to create viral replicates until the
cell burst from high volume of new viral particles. TEs may be duplicated if their
transposition takes place during S phase of the cell cycle when a donor site has
already been replicated. Such duplication at the target site can results in gene
duplications which plays an important role in genomic evolution.
QUESTION 2:

1.Transformation is the process of horizontal gene transfer by which some bacteria

take up foreign genetic material of naked DNA from the environment. If the DNA is in
the form of circular DNA called a plasmid therefore it can be copied in the receiving
cell and passed on to its descendants. Transformation occurs after the restriction
digest and ligation, and it transfers newly made plasmids to bacteria. Therefore, after
the transformation the bacteria is selected on antibiotic plates. The bacteria with a
plasmid are antibiotic-resistance and each one will form a colony. Colonies with the
right plasmid can be grown to make large cultures of identical bacteria which are
used to produce plasmid or make up a protein.

FIGURE 3: shows the structure of DNA transformation.

2.Specialized transduction is the process by which a restricted set of bacterial genes

are transferred to another bacterium. The genes that get transferred depend on
where the phage genome is located on the chromosome. Specialized transduction
occurs when the prophage excises imprecisely from the chromosome so that the
bacterial gene lying adjacent to the prophage are included in the excised DNA. The
excised DNA is then packaged into a new virus particle which can then deliver the
DNA to a new bacterium where the donor genes can be inserted into the recipient
chromosome or remain in the cytoplasm depending on the nature of the
bacteriophage. When the partially encapsuled phage material infects another cell
and becomes a prophage when it is covalently bonded into the infected cells
chromosome the partially coded prophage DNA is called a heterogenote.
Figure 4: shows the structure of specialized transduction.

3. Generalized transduction is the process by which any bacterial gene may be

transferred to another bacterium via bacteriophage and carries only the bacterial
DNA and no viral DNA. In essence this is the packaging of bacterial DNA into a viral
envelope. This may occur in two ways which is recombination and headful
packaging. If bacteriophage undertake the lytic cycle of infection upon entering a
bacterium, then the virus will take control of the cell’s machinery for use in replicating
its own viral DNA. The bacterial chromosome is inserted into the viral capsid which
is usually used to encapsulate the viral DNA. The new virus capsule is loaded with
the part of bacterial DNA which continue to infect another bacterial cell. This
bacterial material may become recombined into another bacterium upon infection.
Figure 5: shows the structure of Generalized transduction.

4.In conjugation the DNA is transferred between bacteria through a tube between
cells which it can also be transferred from one bacterium to another. During
conjugation one bacterium is serves as the donor of the genetic material and the
other serves as the recipient. The donor bacterium carries a DNA sequence that is
called the fertility factor or F- factor. The fertility factor allows the donor to produce a
thin tubelike structure called pilus which the donor uses it to contact the recipient.
The pilus draws the two bacteria together at which time the donor bacterium
transfers genetic material to the recipient bacterium. The genetic material is in the
form of a plasmid or a piece of circular piece of DNA. The genetic material
transferred during conjugation it often provides the recipient bacterium with some
sort of genetic advantage. In some cases, conjugation serves to transfer plasmids
that carry antibiotic resistance genes.
Figure 6 shows the structure of Bacterial conjugation.

Question 3

Antimicrobial resistance occurs when microbes evolve mechanisms that protect

them from the effects of antimicrobials. The main cause of antibiotic resistance is the
antibiotic use which occurs when we use antibiotics there are some bacteria that
dies but resistant bacteria can survive and even multiply. The overuse of this
antibiotic makes the resistance bacteria more common and the more we use
antibiotics the more chances that the bacteria must become resistant to them.
Antibiotics are medicines used to prevent and treat bacterial infections.

Bacteria has evolved to overcome a wide range of antibiotics and resistance

mechanism. Mediated phage is used as a genetic tool which increases the bacterial
susceptibility to antibiotics. Mediated phage of Gram-negative bacterium Escherichia
coli is used to target some several gene networks and rendering the bacteria to be
more sensitive to antibiotics. It is demonstrated that disrupting the sinusoidal
obstruction syndrome (SOS) response by phage-mediated gene targeting renders
the bacteria severalfold more sensitive to a variety of antibiotics. It also
demonstrated that phage-mediated gene transfer combined with antibiotics is used
to increase the survival of infected organism with pathogenic E. coli. The transferring
of genes by phage- mediated gene weakens the bacteria and renders them to be
more susceptible to be killed by antibiotics. the transferred genes target a beneficial
pathway in bacteria and therefore significantly reduce the fitness of the bacteria
harbouring the phage. Consequently, negative selection pressure is constantly being
applied against transfer of these genes by the phage- mediated genes.

Some data suggest that the phage therapy may also enhance a response to
traditional antibiotics either by killing the most drug-resistant strains or by creating a
defensive bacterial response that results in improved antibiotic susceptibility.
Pathogen resistance to antibiotics is a rapidly growing problem which leads to an
urgent need for novel antimicrobial agents. The development of new antibiotics faces
numerous obstacles and a method that desensitizes pathogens to approved
antibiotics therefore holds key advantages. We present a proof of principle for a
system that restores antibiotic efficiency by reversing pathogen resistance. This
system uses temperate phage’s to introduce by lysogenization the genes rpsL and
gyrA conferring sensitivity in a dominant fashion to two antibiotics, streptomycin and
nalidixic acid, respectively.

Unique selective pressure is generated to enrich for bacteria that harbour the phage
carrying the sensitizing constructs. This selection pressure is based on a toxic
compound, tellurite, and therefore does not forfeit any antibiotic for the sensitization
procedure. We further demonstrate a possible way of reducing undesirable
recombination events by synthesizing dominant sensitive genes with major barriers
to homologous recombination. Such synthesis does not significantly reduce the
gene’s sensitization ability. Unlike conventional bacteriophage therapy, the system
does not rely on the phage’s ability to kill pathogens in the infected host, but instead,
on its ability to deliver genetic constructs into the bacteria and thus render them
sensitive to antibiotics prior to host infection. The transfer of the sensitizing cassette
by the constructed phage will significantly enrich for antibiotic-treatable pathogens on
hospital surfaces. Broad usage of the proposed system in contrast to antibiotics and
phage therapy will potentially change the nature of nosocomial infections toward
being more susceptible to antibiotics rather than more resistant.