Posts Tagged ‘ evolution ’

Evolution of Bacterial Virulence

Point Mutations

Much like humans, bacteria are subject to evolution. Evolution occurs through beneficial mutations in the DNA. Because bacteria have much shorter generation times than humans, the process of evolution occurs much more rapidly. An example of how bacteria evolve through mutation is point mutation.

Point mutation is the random mutation of DNA nucleotides which occurs due to incorrect replication of DNA. The types of mutation that can occur are substitution of a nucleotide, deletion of a nucleotide or the addition of a nucleotide. For example, in a sequence of DNA a fragment of which codes for something (such as a protein) consists of multiple codons (sections of 3 nucleotides) if one of these nucleotides is altered in a point mutation, the codon (which codes for a specific amino acid) will be altered. Some alterations of codons will mean they encode for a different amino acid:

Initial DNA:                  … … TTA … …

After point mutation: … … TAA … …

In this case the selected codon in the initial DNA encodes for the amino acid leucine, however after the mutation, it no longer encodes for an amino acid at all as TAA is a stop codon (this closes the reading frame, meaning the rest of the gene is not read).

Point mutations may sometimes have no effect however, as multiple codons can encode for the same amino acid, for example:

Initial DNA:                  … … GCT … …

After point mutation: … … GCA … …

Both GCT and GCA codons encode for the amino acid alanine, so there are no alterations to the final protein which is encoded for by this gene.

Horizontal Gene Transfer

Bacteria are also able to ‘evolve’ by means other than mutation. Horizontal gene transfer is the sharing of genetic information between individuals in the population. Typical gene transfer occurs vertically i.e. parent to offspring, however with horizontal gene transfer genetic information can be spread to completely unrelated individuals.

There are three primary forms of horizontal gene transfer, these are:

  • Transformation – DNA is taken up from the environment
  • Conjugation – DNA is transferred directly between individual bacteria
  • Transduction – DNA transfer is mediated by bacteriophages (a virus which infects bacteria)

Transformation

Many bacteria are naturally transformable and have various means of DNA uptake from their environment. Bacteria able to do this have genes which encode for protein machinery which transports the DNA across the cell membrane from the environment. It is then possible for this DNA to be incorporated into the bacterial chromosome.

This ability has important implications in bacterial pathogenicity for example; Neisseria gonorrhea are able to uptake DNA from the environment which enables them to undergo possible conformational changes that make them more pathogenic. Another example would be Streptococcus pneumoniae and its possibility to acquire penicillin resistance.

Conjugation

Conjugation is the direct transfer of DNA between bacteria, this is of major advantage as advantageous genes (such as those which encode for antibiotic resistance) can be easily spread throughout the population.

DNA is transferred in the form of a plasmid (a circular DNA structure) in a unidirectional manner, that is only the donor requires the plasmid transfer-associated genes (i.e. those which encode for plasmid transfer mediating pili) for horizontal transfer via conjugation to occur.

Plasmids

Plasmids are typically circular in structure and consist of double stranded DNA. They replicate independently of the bacterial chromosome and are located in the cytoplasm, they are usually much smaller than the bacterial chromosome ranging from 1-100kb long. The genes found within the plasmid can be expressed by the bacterium and so proteins encoded for by the plasmid can be formed in the bacterium.

The most common plasmids are those which encode for antibiotic resistance. They are highly prevalent because of the great advantage they give to bacterial survivability. The are multiple genes found on plasmids which promote antibiotic resistance all with different mechanisms of producing resistance.

For example β-lactam antibiotics (such as penicillin derivatives) work by inhibiting cell wall synthesis, however β-lactamase is a bacterial enzyme which breaks the ring structure of these antibiotics are removes their antibacterial properties. These enzyme is encoded for by genes found within plasmids, which can easily be spread around the population thus increasing the resistance of the population to β-lactam antibiotics.

Other forms of plasmid-conferred attributes include:

  • Bacteriocins – Proteinaceous toxins which inhibit the growth of competitor species a specific example of this is colicin, a bacteriocin produced by Escherichia coli which exerts a cytotoxic effect within competitor species’ cytoplasm.
  • Toxin production – Toxins which affect other species such as the heat-labile enterotoxin produced by E. coli which causes diarrhoea or the Clostridium tetani tetanus toxin, the neurotoxin responsible for causing tetanus.
  • Protein delivery systems – Such as the Yersinia pestis secretion system, which allows them to inject protein materials into other organisms (such as immune cells), these injected proteins are known as YOPs (Yersinia outer proteins).
  • Adhesins – Typically pili (protein surface projections) which allow adherence to bind to cells, which is important in pathogenicity. Such adhesins can be found in E. coli and Shigella.
  • Metabolic activities – For example, the ability of Salmonella species to ferment lactose

Transduction

Transduction is the transfer of DNA which is mediated by bacteriophages (viruses which infect bacteria, combining their DNA with the bacterium host). Many bacteriophages have both lytic and lysogenic cycles of reproduction (typically viruses are one or the other). The lytic cycle is where the virus enters the cell, replicates using the cell’s own machinery and then lyses the cell releases large numbers of virus. The lysogenic cycle is where the virus incorporates its genetic material into the cell where it lies dormant until a later date, the viral genes are replicated when the cell replicates allowing them to reactivate and continue into a lytic cycle (formation of phages).

Bacteriophage-encoded virulence factors include:

  • Streptococcus pyogenes toxin (which causes scarlet fever)
  • Corynebacterium diphtheriae toxin
  • Clostridium botulinum toxin

E. coli O157:H7 contains around 1.4Mb of extra DNA when compared to E. coli K12 (a much less pathogenic strain which is used in laboratories). It is suggested that around 50% of this extra genetic material has been derived from bacteriophages.

Vibrio cholera Toxin

Another bacteriophage encoded virulence factor is the Vibrio cholera toxin, however for this toxin to be produced by the bacterium, genetic material from two bacteriophages must be acquired.

The initial bacteriophage (VPI phage) infects a non-toxic Vibrio cholera bacterium, its transduced genetic material encodes for pili proteins which act as an attachment site for the secondary bacteriophage (CTX phage). When CTX phage binds, the genetic material it incorporates encodes for the production of the cholera toxin and thus the bacterium becomes toxogenic.

Recombination

Transformed and transduced (i.e. non-plasmid DNA) is inserted into the recipient bacterial chromosome by recombination. Recombination is also responsible for the rearrangement of DNA fragments around the genome (genomic plasticity) which enables the bacteria to survive in rapidly changing environments due to the alterations in the genes which are expressed. Recombination can be either homologous (RecA dependent – a DNA repair and maintenance protein) or non-homologous.

Homologous Recombination

DNA inserted into the bacterium can be incorporated into the bacterial chromosome if there are regions of homology expressed on both the foreign transmitted DNA and the bacterial chromosome DNA. The differences between the foreign and bacterial DNA will cause RecA to attempt to ‘repair’ the chromosome. In doing so, the foreign DNA may be incorporated into the bacterial chromosome, (there is also the chance that it will be disregarded).

Non-homologous Recombination

Non-homologous recombination allows genetic material to enter the bacterial chromosome without RecA. Small fragments of DNA known as insertion sequences (ISs) are what enter the chromosome. ISs typically consist of DNA fragments from bacteriophages or elsewhere, however, all that an IS codes for is its motility and insertion. ISs integrate into the bacterial chromosome through self-encoded transposition enzymes (as opposed to RecA) and when within the chromosome they facilitate replication of themselves. The short ISs then become numerous within the bacterial chromosome.

The presence of multiple ISs within the bacterial chromosome is what allows genetic plasticity (The movement or deletion of short fragments of DNA within the chromosome). Genetic plasticity leads to alterations in genes or the removal of genes altogether, this has the potential to increase pathogenicity. For example, Bordetella bronchiseptica is a gram negative bacterium responsible for causing infectious bronchitis, which rarely infects humans. B. pertussis on the hand is the major causative agent of pertussis (whooping cough) and is an obligate human pathogen. It is believed that genetic plasticity caused a reshuffling of the B. bronchiseptica chromosome which lead to the formation of the obligate human pathogen B. pertussis.

Transposons

Transposons are transmitted by similar means to ISs, however they are more structurally complex and much larger, due to the greater amount of genetic information they carry. This extra genetic material encodes for attributes such as antibiotic resistance, toxins and enzymes.

Some transposons (known as conjugative transposons) excise themselves from the bacterial chromosome to form circular intermediates of DNA, much like plasmids. These can also be transmitted around a population, again like plasmids, to spread resistance to antibiotics etc.

Pathogenicity Islands

Pathogenetic islands are also laterally-transmitted. They are large integrated DNA elements which carry multiple virulence-associated genes such as those which encode for adherence factors, secretion systems, toxins and invasion factors. A bacterium may have multiple pathogenicity islands and due to the incorporation of multiple virulence factors on one island, the transmission of one island often causes a non-toxogenic bacterium to become pathogenic.

They may be incorporated into the main bacterial chromosome or any plasmids which may be present in the cytoplasm, the DNA found within these islands may contain remnants from bacteriophages and IS elements. The GC-content (guanine-cytosine content) is often different from the rest of the genome.

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Evolution of Animal Fighting Behaviour

It is recommended that you read ‘An Introduction to the Evolution of Animal Fighting Behaviour‘ before you read this, as there are some concepts explained in the earlier article which are used without explanation in this article.

Introduction

Success in fighting behaviour is frequency dependent i.e. as the population size increases fighting success decreases. Fighting behaviour amongst a species is often explained in terms of roles, for example we have previously looked at the fairly simplistic Hawk/Dove model which gives animals the role of either hawk or dove.

When determining which strategy will be dominant amongst a population we check it against the ‘standard conditions’ of Maynard Smith. If a strategy is adopted amongst the majority of a population we call it an evolutionarily stable strategy (ESS). An ESS is a strategy which, if adopted by most members of a population, cannot be invaded by a mutant strategy which is initially rare. The standard conditions to determine if a strategy (e.g. strategy I) is an ESS are:

Either:

1 – E (I, I) > E (J, I)

Or

2 – If E (I, I) = E (J, I) then E (I, J) > E (J, J)

E (I, I) is the payoff of strategy I against strategy I. Therefore by the conditions of 1, strategy I is an ESS if the payoff of I vs. I is greater than the payoff J receives from fighting I i.e. E (J, I).

The Hawk/Dove/Retaliator Model

The Hawk/Dove model makes certain assumptions:

  • Animals fight with equal ability
  • Animals fight in pairs
  • Animals can only display, escalate or retreat
  • Encounters are random

Due to the limitations of the Hawk/Dove model an additional strategy was added – retaliator

  • Hawks (H)– Escalate immediately, retreat if injured
  • Doves (D)– Display immediately, retreat if opponent escalates
  • Retaliators (R)– Immediately display, escalate if opponent escalates and retreat if injured

The payoff matrix looks like this:

Vs. > H D R
H (V-C)/2 V (V-C)/2
D 0 V/2 (V/2)x 0.9
R (V-C)/2 (V/2)x 1.1 V/2
  • V = Value of resource.
  • C = Cost paid attempting to gain resource.
  • The reason for the x1.1 is that retaliators do slightly better than doves (10%) as they sometime escalate so their payoff is increased.
  • The reason for the x0.9 is the same as above, but because the doves sometimes lose, their payoff is reduced by 10%.

When V>C: Hawk is not an ESS, doves are unable to invade and therefore retaliator is an ESS.

When V<C: Hawk is not an ESS, doves are unable to invade and therefore retaliator is an ESS.

The War of Attrition

When 2 animals meet in a contest for a resource, the amount of energy they are willing to invest to win that resource are predetermined. The animal will therefore display until this time/energy is up. This value is not modified during the display. In the contest, the animal which wins is therefore the one who invested the most predetermined energy. We can model this:

  • Rate of cost accumulation: c
  • Contest length: T
  • Cost of contest: cT
  • Resource value: V
  • Animal A persistence time: TA
  • Animal B persistence time: TB

In this example TA > TB

Payoff to animal A = V – cTB (Animal A wins the resource V but still has to pay the cost, c for the length of the contest, the length of the contest would therefore be TB as the contest ended when animal B gave in.)

Payoff to animal B = – cTB (Animal B does not win any resource, but must still pay the energy that was used during the contest)

A population does not evolve a constant persistence time, however:

  • If cT < V it is worth persisting longer for a resource as the payoff is greater than the cost.
  • If cT > V then a persistence time of 0 spreads amongst the population as to engage in contest for the resource will mean a loss of energy (even if winning). It is therefore better to not engage and lose nothing.

The length animals choose as their persistence time follows a negative exponential distribution, i.e. many choose short times and a very limited number choose long times. The length of contests will therefore also follow this distribution. The log of the number of contests plotted against the length of the contests will give a straight line.

Examples:

  • Damselfly larvae compete for perching space. Intruders encroaching on perching space will be warned by a ritualised display of the abdomen. The intruder may either leave or contest against the perch space owner. The contests are slow, but their duration follows the negative exponential predicted earlier, however 70-80% of the contests are won by the original occupant and not the 50% you would expect.
  • The fighting of male dungfly over female dungfly (which can be considered a resource) follows the same negative exponential pattern.

The assumption that all contests are fought symmetrically (equal chances of winning) is false, we can assume asymmetry because:

  • Resource Value – Resources are worth more or less to different animals, e.g. a piece of food may be worth more to a hungry animal than a recently fed animal.
  • Resource Holding Power (RHP) – The fighting ability of the animal, this will vary amongst the population, those with a higher RHP will be more likely to win a contest.
  • Uncorrelated Asymmetry – This is any asymmetry which is not correlated to the value of the resource.

Resource Holding Power (RHP):

  • RHP is the fighting ability of an animal, therefore the animal with the greatest RHP is going to keep the resource and the animal with the lower RHP will retreat.
  • Animals must therefore find a way to assess the RHP of others.
  • If RHPs are of similar value, this is when a fight will escalate.
  • For example:
    • The roar contest in red deer helps to determine the RHP. The deer with the lower roaring rate retreats as it is very likely to have a lower RHP. This type of contest is a true signal of RHP (unlike size for example).
    • Croaking in toads when trying to find/compete for a female allows the toads to determine RHP and thus whether or not to attack. Larger males produce deeper croaks and are determined to have a higher RHP.

Bourgeois Strategy

The Bourgeois strategy is a method used to determine the payoff values for competing for resources. It is substituted into the Hawk/Dove model. The Bourgeois strategy is:

  • If it is the owner of a resource, it plays hawk
  • If it is the intruder, it plays dove
  • The assumption is 50% of the time; the Bourgeois is the owner of the resource.

When we put this into a payoff matrix we get the results:

  • If V>C – The hawk strategy is an ESS
  • If V<C – The Bourgeois strategy is an ESS

e.g. The speckled wood butterfly protect areas of sunlight as they are looking for a mate. When an intruder approaches a short spiral fight occurs. The owner of the path of sunlight always wins the spiral fight. If there is confusion over the ownership of the sunlight patch then the spiral fight lasts much longer.

There also exists an Anti-Bourgeois strategy where the intruder always wins the resource for example:

  • In certain spider species, intruders always displace the owner of a web funnel.
  • Seagulls on a flag post always give up the space immediately to invaders.