New iDynoMiCS plasmid model
The plasmid model in iDynoMiCS is a very simple one, containing only the relevant methods to ensure
the continuation and transmission of plasmids to other agents.
iDynoMiCS’ EpiBac class makes it possible for the agent to host plasmids and other EPS. This class
prepared for an agent of this class to hold more than one plasmid, by instantiating the Episome lass and
storing these instances in a list. However, the Episome class, or the plasmid class, functions as an
indivisible individual, which defeats the modular nature of a plasmid; therefore, to ensure modularity
and ease of implementation, the plasmid was divided in two parts concerning functionality: the first
part, known as the backbone (encapsulated in OriginOfTransfer class), relates to the defining of the
transfer machinery; this part will contain the necessary items required for conjugation. The second is
where all the genes are encoded into the plasmid. The Episome class manages both.
The backbone module is where all the necessary information for the plasmid main operation is
contained: the Origin of Transfer (oriT), T4SS and MOB genes. This section will only incorporate the
required elements for conjugation, protein-producing and reporter genes are stored elsewhere. This
structure allows the simulation of distinct plasmid types; if in this section the plasmid lacks any of the
substances required by the protocol file, and it can’t find them expressed or within the bacterium, the
plasmid becomes non-mobilizable and can only be transferred via segregation. On the contrary, if the
bacterium has all listed substances in enough concentration, also specified in the protocol file, the
plasmid is considered a mobilizable-conjugative plasmid, whether or not the plasmid’s own genes are
the ones expressing the substances.
All the MOB required substances will be treated as proteins, with the exception of oriT and T4SS. For
otiT, only its existence in the plasmid will be checked, since is one of the first conditions to be examined
while in conjugation. T4SS have to be encoded and expressed in a gene, but will not be conditioned to a
certain concentration threshold. Also, a plasmid can have one or more oriT, T4SS, and Mob machinery
configured.
The genes that form the plasmid body can be of two types: protein-producer or a reporter. Additional
gene types may be introduced seamlessly. As instance of Gene class, the genes have a promoter zone
that designates a logical condition to be met; this in turn expresses or inhibits the production of protein
or fluorescence.
The proteins accumulate its concentration within the host up until the maximum permitted amount
dictated by the protocol file. These substances also have a limited lifespan, after a certain time a protein
will start degrading and will cease its existence inside the host cell if the gene responsible for its
production is inhibited. The concentration management of the proteins is done by the ProteinContainer
and Gene classes. Also, the backbone module may require the presence of certain proteins, and thus, be
treated the same as the inhibition-activation function and resolved by a special class called Parser.
All the substances that are expressed through the genes are stored in the host. This means that the
EpiBac class will now have the task of maintaining the concentrations of substances in its interior. For
this, a special container class was designed, in which all the individual proteins are managed called
ProteinController which is very similar to iDynoMiCS own AgentContainer class.
The Parser class verifies the conditional of both the genes expression and the backbone requirements,
measuring the presence and concentration of all required proteins or genes present inside the plasmid
of cell.
Plasmid compatibility only allows certain plasmids to coexist with one another, that is, plasmids bearing
a particular CompatibilityMarker may be permitted inside a recipient cell as long as the plasmid already
there has a different marker. To enhance this type compatibility of plasmids, a series of improvements
were built. This allows, by protocol file configuration, for a plasmid marked with a certain
CompatibilityMarker to be compatible with only certain other markers while discriminating the others.
This function can be either configured or not and does not conflict with any other function in the
simulator.
To fine tune the overall conjugation process, several small adjustments were made to EpiBac class. Such
as the inclusion of a maturity time lag, that calculates the probability of a conjugation depending on the
current age of the host. And also a routine that adjust the growth rate of the transconjugant cell to take
into account the metabolic burden a plasmid makes on its host. Both of these features are configured in
the protocol file and, if not present, make no effect in the flow of simulation.
UML diagram of the new plasmid model
UML DIAGRAM OF THE IDYNOMICS PLASMID EXTENSION.
This is the final UML class diagram of the new model; all the new classes were added in a package called
extension inside simulator.agent package. The classes shown in the diagram are explained below:
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EpiBac – Host class, this class will be the one managing plasmids, proteins and conjugation.
Episome – Class hosting the plasmid, manages genes encoded in it.
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EpisomeParam – This class extracts the needed information from the protocol file and sets the
required variables.
OriginOfTransfer – This class stores the backbone part of the plasmid-model, is where the
conditions for conjugation are stored
Gene – represents a gene encoded into the plasmid
ProteinContainer – manages the proteins that exists within the hosts
Protein – represents a type of protein in the bacterium, its concentration varies with time.
Parser – this class parses the promoter and backbone conditions with the existences of protein
Promoter – in this stored the condition that regulates the gene’s expression