Case 3: What is the difference
between commensals and
pathogens?
KEYWORDS
- Horizontal Gene Transfer (Transformation, Conjugation, Specialized/Generalized
Transduction, Vesiduction)
- Mobile Genetic Elements (Insertion Sequences, Composite Transposons, Unit
Transposons, Bacteriophages, Conjugative Plasmids, Integrative and Conjugative
Elements (ICE's))
- Comperative Genomics (Core genome, Pangenome, pathogenicity Islands)
- Secretion Systems (T3SS, T4SS, T6SS)
- Adhesion Factors
- Invasion/dissemination Factors
- Biofilm formation
- Iron Scavenging
- Toxin
HORIZONTAL GENE TRANSFER
Bacteria and archaea do not reproduce sexually. This suggests that genetic variation in populations of
these microbes should be relatively limited, only occurring with the advent of a new mutation and its
passage to the next generation by vertical gene transfer. However, this is not the case. Bacteria and
archaea have multiple mechanisms for creating recombinants collectively referred to as horizontal
(lateral) gene transfer (HGT). HGT is distinct from vertical gene transfer because genes from one
independent, mature organism are transferred to another mature organism, often creating a stable
recombinant having characteristics of both donor and recipient.
,HGT is the main mechanism by which bacteria and archaea evolve. Many examples of DNA transfer
between distantly related genera and across domains of life are known, particularly among microbes
sharing a habitat (e.g., the human gut). HGT helps bacteria and archaea survive environmental
stresses. For instance, some archaea respond to UV radiation by increasing their ability to carry out
HGT so that they can obtain and use DNA from other cells to repair UV-damaged DNA in their
genomes. Another important example is the transfer of groups of genes encoding virulence factors
from pathogens to other bacteria. These gene clusters are called pathogenicity islands, and their
discovery has provided valuable insights into the evolution of pathogenic bacteria. Finally, in most
cases, the acquisition of new traits by HGT enables microbes to rapidly expand their ecological niche.
This is clearly seen when HGT results in the spread of antibiotic-resistance genes among bacteria.
HGT in bacteria occurs through three mechanisms. DNA may be acquired directly from the
environment (transformation), it may be transferred from a donor cell (conjugation), or it may be
transported in a bacteriophage (transduction). HGT in archaea has been documented using the same
mechanisms, and a few others. Structures like nanotubes or membrane vesicles also mediate DNA
transfer in both domains. (The term vesiduction has been proposed for vesicle transport of DNA.) The
multiple and varied mechanisms of HGT illustrate that the gene pool for bacteria and archaea is both
external and vast.
During HGT, a piece of donor DNA enters a recipient. The donor DNA has four possible fates in the
recipient. First, when the donor DNA has a sequence homologous to the recipient’s chromosome,
integration may occur. The donor DNA may pair with the recipient DNA and recombine. The
recombinant then reproduces, yielding a population of stable genetic variants. Second, if the donor
DNA is able to replicate (e.g., it is a plasmid), it may persist separate from the recipient’s
,chromosome. When the recipient reproduces, the donor DNA replicates, and a population of stable
recombinants is formed. Third, the donor DNA remains in the cytoplasm but is unable to replicate.
After multiple cell divisions, the donor DNA is eventually lost from the population. Finally, host
restriction or CRISPR/Cas degradation of donor DNA may occur, thereby preventing the formation of
a recombinant cell.
Homologuous recombination
Crossing-over during meiosis in eukaryotes and integration of donor DNA into the recipient’s
chromosome during HGT in bacteria and archaea occur by similar mechanisms. Homologous
recombination is the most common mechanism, and many of the enzymes used are similar in all
organisms. Homologous recombination occurs wherever there are long regions of the same or similar
nucleotide sequence in two DNA molecules (e.g., sister chromosomes in diploid eukaryotes or similar
sequences on both a chromosome and plasmid). Homologous recombination results from DNA
strand breakage and reunion leading to crossing-over. It is carried out by enzymes, many of which
are also important for DNA repair.
The other major type of recombination is site-specific recombination. Site-specific recombination
differs from homologous recombination in three significant ways. First, it does not require long
regions of sequence homology. Second, recombination occurs at specific target sites in DNA
molecules, and third, it is catalyzed by enzymes collectively called recombinases. Site-specific
recombination is the mechanism by which some plasmids and viral genomes integrate into host
chromosomes. It is also the type of recombination used by mobile genetic elements to move from
one place to another in DNA molecules.
Transposition (done)
As genomes are sequenced and annotated, it is apparent that they are rife with genetic elements
that move within and between genomes. These elements are referred to as “jumping genes,” mobile
genetic elements, or transposable elements. Transposition refers to the movement of such an
element. Mobile genetic elements (MGEs) promote DNA mobility both within a cell and between
cells. The many types of MGE differ in structure, mechanisms of integration and excision, and ability
, to be transferred from one cell to another by HGT. The enzymes that function in transposition are
collectively termed recombinases. However, the recombinase used by a specific MGE may be called
an integrase, resolvase, or transposase. MGE insertions are random, occurring at any site in a
genome.
The simplest MGEs are insertion sequences or IS elements. An IS element is a short sequence of DNA
(around 750 to 1,600 base pairs [bp] in length). It typically contains only the gene for transposase,
and it is bounded at both ends by inverted repeats—identical or very similar sequences of
nucleotides in reversed orientation. Inverted repeats are usually about 15 to 25 bp long and vary
among IS elements so that each type of IS has a specific nucleotide sequence in its inverted repeats.
Transposase recognizes the ends of the IS and catalyzes transposition. IS elements have been
documented in many bacteria and some archaea.
Transposons are more complex in structure than IS elements. Composite transposons consist of a
central region containing genes unrelated to transposition (e.g., antibiotic-resistance genes) flanked
by IS elements that are identical or very similar in sequence (figure 16.11b). The flanking IS elements
encode the transposase used by the transposon to move. Many IS carry strong promoters that
activate nearby genes. Unit transposons are bounded by inverted repeats, but lack IS elements. They
encode their own transposase and often carry passenger genes.
between commensals and
pathogens?
KEYWORDS
- Horizontal Gene Transfer (Transformation, Conjugation, Specialized/Generalized
Transduction, Vesiduction)
- Mobile Genetic Elements (Insertion Sequences, Composite Transposons, Unit
Transposons, Bacteriophages, Conjugative Plasmids, Integrative and Conjugative
Elements (ICE's))
- Comperative Genomics (Core genome, Pangenome, pathogenicity Islands)
- Secretion Systems (T3SS, T4SS, T6SS)
- Adhesion Factors
- Invasion/dissemination Factors
- Biofilm formation
- Iron Scavenging
- Toxin
HORIZONTAL GENE TRANSFER
Bacteria and archaea do not reproduce sexually. This suggests that genetic variation in populations of
these microbes should be relatively limited, only occurring with the advent of a new mutation and its
passage to the next generation by vertical gene transfer. However, this is not the case. Bacteria and
archaea have multiple mechanisms for creating recombinants collectively referred to as horizontal
(lateral) gene transfer (HGT). HGT is distinct from vertical gene transfer because genes from one
independent, mature organism are transferred to another mature organism, often creating a stable
recombinant having characteristics of both donor and recipient.
,HGT is the main mechanism by which bacteria and archaea evolve. Many examples of DNA transfer
between distantly related genera and across domains of life are known, particularly among microbes
sharing a habitat (e.g., the human gut). HGT helps bacteria and archaea survive environmental
stresses. For instance, some archaea respond to UV radiation by increasing their ability to carry out
HGT so that they can obtain and use DNA from other cells to repair UV-damaged DNA in their
genomes. Another important example is the transfer of groups of genes encoding virulence factors
from pathogens to other bacteria. These gene clusters are called pathogenicity islands, and their
discovery has provided valuable insights into the evolution of pathogenic bacteria. Finally, in most
cases, the acquisition of new traits by HGT enables microbes to rapidly expand their ecological niche.
This is clearly seen when HGT results in the spread of antibiotic-resistance genes among bacteria.
HGT in bacteria occurs through three mechanisms. DNA may be acquired directly from the
environment (transformation), it may be transferred from a donor cell (conjugation), or it may be
transported in a bacteriophage (transduction). HGT in archaea has been documented using the same
mechanisms, and a few others. Structures like nanotubes or membrane vesicles also mediate DNA
transfer in both domains. (The term vesiduction has been proposed for vesicle transport of DNA.) The
multiple and varied mechanisms of HGT illustrate that the gene pool for bacteria and archaea is both
external and vast.
During HGT, a piece of donor DNA enters a recipient. The donor DNA has four possible fates in the
recipient. First, when the donor DNA has a sequence homologous to the recipient’s chromosome,
integration may occur. The donor DNA may pair with the recipient DNA and recombine. The
recombinant then reproduces, yielding a population of stable genetic variants. Second, if the donor
DNA is able to replicate (e.g., it is a plasmid), it may persist separate from the recipient’s
,chromosome. When the recipient reproduces, the donor DNA replicates, and a population of stable
recombinants is formed. Third, the donor DNA remains in the cytoplasm but is unable to replicate.
After multiple cell divisions, the donor DNA is eventually lost from the population. Finally, host
restriction or CRISPR/Cas degradation of donor DNA may occur, thereby preventing the formation of
a recombinant cell.
Homologuous recombination
Crossing-over during meiosis in eukaryotes and integration of donor DNA into the recipient’s
chromosome during HGT in bacteria and archaea occur by similar mechanisms. Homologous
recombination is the most common mechanism, and many of the enzymes used are similar in all
organisms. Homologous recombination occurs wherever there are long regions of the same or similar
nucleotide sequence in two DNA molecules (e.g., sister chromosomes in diploid eukaryotes or similar
sequences on both a chromosome and plasmid). Homologous recombination results from DNA
strand breakage and reunion leading to crossing-over. It is carried out by enzymes, many of which
are also important for DNA repair.
The other major type of recombination is site-specific recombination. Site-specific recombination
differs from homologous recombination in three significant ways. First, it does not require long
regions of sequence homology. Second, recombination occurs at specific target sites in DNA
molecules, and third, it is catalyzed by enzymes collectively called recombinases. Site-specific
recombination is the mechanism by which some plasmids and viral genomes integrate into host
chromosomes. It is also the type of recombination used by mobile genetic elements to move from
one place to another in DNA molecules.
Transposition (done)
As genomes are sequenced and annotated, it is apparent that they are rife with genetic elements
that move within and between genomes. These elements are referred to as “jumping genes,” mobile
genetic elements, or transposable elements. Transposition refers to the movement of such an
element. Mobile genetic elements (MGEs) promote DNA mobility both within a cell and between
cells. The many types of MGE differ in structure, mechanisms of integration and excision, and ability
, to be transferred from one cell to another by HGT. The enzymes that function in transposition are
collectively termed recombinases. However, the recombinase used by a specific MGE may be called
an integrase, resolvase, or transposase. MGE insertions are random, occurring at any site in a
genome.
The simplest MGEs are insertion sequences or IS elements. An IS element is a short sequence of DNA
(around 750 to 1,600 base pairs [bp] in length). It typically contains only the gene for transposase,
and it is bounded at both ends by inverted repeats—identical or very similar sequences of
nucleotides in reversed orientation. Inverted repeats are usually about 15 to 25 bp long and vary
among IS elements so that each type of IS has a specific nucleotide sequence in its inverted repeats.
Transposase recognizes the ends of the IS and catalyzes transposition. IS elements have been
documented in many bacteria and some archaea.
Transposons are more complex in structure than IS elements. Composite transposons consist of a
central region containing genes unrelated to transposition (e.g., antibiotic-resistance genes) flanked
by IS elements that are identical or very similar in sequence (figure 16.11b). The flanking IS elements
encode the transposase used by the transposon to move. Many IS carry strong promoters that
activate nearby genes. Unit transposons are bounded by inverted repeats, but lack IS elements. They
encode their own transposase and often carry passenger genes.
