biocrnpyler.mechanisms.Transcription_MM

class biocrnpyler.mechanisms.Transcription_MM(rnap: Species, name='transcription_mm', **kwargs)[source]

Bases: MichaelisMentenCopy

Michaelis-Menten transcription with explicit RNA polymerase.

A ‘transcription’ mechanism that explicitly models RNA polymerase (RNAP) binding to DNA, followed by transcription and release. This mechanism follows Michaelis-Menten kinetics and is appropriate when RNAP is limiting or when explicit modeling of polymerase-DNA interactions is needed.

The reaction follows the schema:

\[{\text{G}} + {\text{RNAP}} \rightleftharpoons {\text{G}}\mathord{:}{\text{RNAP}} \rightarrow {\text{G}} + {\text{RNAP}} + {\text{mRNA}} \]

Parameters:

  • rnap (Species) – RNA polymerase species that catalyzes transcription.

  • name (str, default 'transcription_mm') – Name identifier for this mechanism instance.

Attributes:

  • rnap (Species) – The RNA polymerase species.

  • name (str) – Name of the mechanism instance.

  • mechanism_type (str) – Type classification (‘transcription’).

See also

SimpleTranscription

Simple transcription without explicit RNAP.

Translation_MM

Michaelis-Menten translation.

MichaelisMentenCopy

Base class for MM copy mechanisms.

Mechanism

Base class for all mechanisms.

Notes

This mechanism models transcription using standard Michaelis-Menten kinetics where RNA polymerase acts as an enzyme that binds DNA, catalyzes mRNA synthesis, and is released unchanged. This is appropriate when:

  • RNAP concentration affects transcription rate

  • Explicit modeling of RNAP-DNA binding is important

  • RNAP sequestration or competition effects are relevant

The mechanism uses the MichaelisMentenCopy base class which generates:

  1. Reversible binding: DNA + RNAP \(\rightleftharpoons\) DNA:RNAP (rates: ‘kb’, ‘ku’)

  2. Catalysis: DNA:RNAP \(\rightarrow\) DNA + RNAP + mRNA (rate: ‘ktx’)

Common applications include:

  • TX-TL systems with limited RNAP

  • Models of transcriptional resource allocation

  • Competition between promoters for RNAP

  • Detailed mechanistic models of gene expression

Required parameters for this mechanism:

  • ‘ktx’ : Transcription/catalysis rate constant

  • ‘kb’ : Forward binding rate for RNAP to DNA

  • ‘ku’ : Reverse unbinding rate for RNAP from DNA

Examples

Model transcription with explicit RNA polymerase:

>>> gene = bcp.DNAassembly(
...     name='gene_assembly',
...     promoter='pconst', transcript='mRNA')
>>> mechanism = bcp.Transcription_MM(rnap=rnap)
>>> mixture = bcp.Mixture(
...     components=[gene],
...     mechanisms={'transcription': mechanism},
...     parameters={'ktx': 0.05, 'kb': 1.0, 'ku': 0.1}
... )
>>> mixture.compile_crn()

Methods

update_reactions

Generate reactions for Michaelis-Menten transcription.

update_species

Generate species for Michaelis-Menten transcription.
update_reactions(dna, component, part_id=None, complex=None, transcript=None, protein=None, **kwargs)[source]

Generate reactions for Michaelis-Menten transcription.

Creates Michaelis-Menten transcription reactions including reversible RNAP-DNA binding and catalytic transcript production.

Parameters:

  • dna (Species) – The DNA species (gene) being transcribed.

  • component (Component) – Component containing parameter values. Required for parameter lookup.

  • part_id (str, optional) – Identifier for parameter lookup. If None, defaults to component.name.

  • complex (Complex, optional) – Pre-specified DNA:RNAP complex species. If None, automatically created.

  • transcript (Species, optional) – The mRNA transcript species produced. If None and protein is provided, protein is produced directly.

  • protein (Species, optional) – Protein species for expression mixtures.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List of two reactions:

  • Reversible RNAP-DNA binding (rates: ‘kb’, ‘ku’)

  • Catalytic transcription (rate: ‘ktx’)

Return type:

list of Reaction

Notes

The reactions follow the Michaelis-Menten scheme:

  1. DNA + RNAP \(\rightleftharpoons\) DNA:RNAP (rates: ‘kb’ and ‘ku’)

  2. DNA:RNAP \(\rightarrow\) DNA + RNAP + Product (rate: ‘ktx’)

Where Product is either transcript or protein depending on mixture type.

update_species(dna, transcript=None, protein=None, **kwargs)[source]

Generate species for Michaelis-Menten transcription.

Creates species involved in RNAP-mediated transcription including DNA, RNAP, the DNA:RNAP complex, and transcript or protein product.

Parameters:

  • dna (Species) – The DNA species (gene) being transcribed.

  • transcript (Species, optional) – The mRNA transcript species produced. If None and protein is provided, protein is produced directly (for expression mixtures).

  • protein (Species, optional) – Protein species for expression mixtures without explicit transcription.

  • **kwargs – Additional keyword arguments (unused).

Returns:

List containing [dna, rnap, dna:rnap complex, product] where product is either transcript or protein.

Return type:

list of Species