I recently read an interesting paper on the competence of bacteria [1]. In this blog post, I’d like to share the main takeaways. The paper focuses on the competence of lactic acid bacteria (LAB), but I will focus only on the competence-related principles mentioned there. These are just my notes, but hopefully, you’ll find them useful.
What is bacterial competence?
It is a specialized physiological state in which bacteria can take up foreign DNA from the environment (also known as transformation). It is a naturally occurring process observed in several species.
What is horizontal gene transfer (HGT)?
It is the transfer of genetic material between different organisms. It is different than the typical parent–offspring transfer of genetic material. It is especially common in bacteria.
What is transduction?
It is a type of HGT, in which genetic material is moved from one bacterium to another by a virus.
What is conjugation?
It is a type of HGT, in which genetic material is moved from one bacterium to another by a tube between those cells. This tube is called a pilus.
What is natural transformation?
It is a type of HGT, in which a competent bacterium takes up DNA from the environment. It is known as the most common type of HGT.
How are competence, horizontal gene transfer (HGT), transduction, conjugation, and natural transformation related?
Transduction, conjugation, and natural transformation are all types of HGT. Natural transformation needs the cell to reach the state of competence to occur.
How is competence achieved?
Competence can be achieved in two ways. Either by each cell separately or by the whole population as a response to signal molecules. The latter is known as quorum sensing.
What are the stages of competence development?
Competence development is divided into two main stages – early and late. Below, I am describing both briefly.
Early phase of competence development
Activation and Expression of Early Competence Genes: Involves the induction of the transcription of competence-specific regulator genes, such as comX in streptococci or comK in Bacillus subtilis.
Late Phase of Competence Development
Activation and Expression of Late Competence Genes: The products of the early competence genes activate the late competence gene. Expression of the late competence genes is necessary for the uptake and integration of DNA from the environment.
DNA Uptake: The pseudopilus-like structure binds and transports exogenous DNA into the cell, a critical component of the late stage.
DNA Processing: Inside the cell, the DNA is processed by proteins for integration or replication. This includes the degradation of non-integrative DNA and the protection of DNA to be integrated.
Integration of Exogenous DNA: Proteins facilitate the integration of the exogenous DNA into the host genome through homologous recombination.
Termination of Competence: Finally, the competence state is terminated, often through the degradation of key competence proteins, preventing continuous DNA uptake and ensuring the cell returns to a non-competent state.
What are the risks related to natural competence and how do bacteria deal with them?
The main risk is that natural competence might introduce potentially harmful genetic changes. To handle that, most species only allow natural transformation to take place when specific conditions occur and some only take up DNA similar to their own.
How was the bioinformatical analysis of competence genes performed?
It appears to be a typical comparative genomics analysis. The authors had data from 173 species and they did the following:
- All-against-all, bidirectional BLAST; it means that all combinations of the sequences were compared with each other
- Markov Clustering (mclblastline pipeline v12-0678) with three different species as references; it was employed to cluster the species based on the conservation of late competence genes within each species
- Results of Markov Clustering were formatted into presence/absence matrices and hierarchical clustering, which was then visualized
This post is obviously very different than all the other ones. Let me know if you like this Q&A paper summary format and if there are any other papers you’d like me to summarize.
References:
[1] Natural Transformation in Gram-Positive Bacteria and Its Biotechnological Relevance to Lactic Acid Bacteria
Laura M. O’Connell, Philip Kelleher, Irma M.H. van Rijswijck, Paul de Waal, Noël N.M.E. van Peij, Jennifer Mahony, Douwe van Sinderen; Annual Review of Food Science and Technology 2022 13:1, 409-431
