New insights into the bacterial immune system

MksBEFG – the protection system is widespread. (A) Representation of mksFEBG-operon organization from different organisms: (i) C. glutamicum ATCC13032, (ii) M. smegmatis mc2 155, (iii) P. aeruginosa UCBPP-PA14 and (iv) P. putida KT24. (B) Plasmid copy numbers of low-copy (pBHK18) and high-copy-number (pJC1) plasmids relative to oriC numbers per cell, assessed by qPCR. Ratios were compared between C. glutamicum WT (MB001), ΔmksB, ΔmksG, ΔmksF cells grown in BHI medium with selective antibiotic (mean ± SD, n = 3). Plasmids pBHK18 and pJC1 were extracted from C. glutamicum WT, ΔmksB, ΔmksG, ΔmksF cells grown in BHI medium with antibiotic selection, visualization of extracted DNA on 0.8% agarose gel. (C) Phylogenetic analysis of MksG-like proteins (organized into DUF3322 and DUF2220 domains) using the SMART platform reveals distribution among Gram-negative and Gram-positive bacteria and archaea. Credit: Nucleic Acids Research (2023). DOI: 10.1093/nar/gkad130

A research team from the University of Kiel describes a previously unknown defense mechanism in bacteria that selectively removes foreign and potentially harmful genetic information.

Since the coronavirus pandemic, the particularly rapid evolutionary adaptability of microorganisms such as bacteria or viruses has been thrust into the public spotlight. For example, when viruses develop the ability to infect new host organisms or bacteria develop resistance to antibiotics, the acquisition of new genetic information from other microorganisms allows them to quickly express advantageous evolutionary traits.

Bacteria, for example, acquire foreign DNA through a process called horizontal gene transfer, which is much faster than vertical inheritance from generation to generation.

However, any living organism also faces risks by receiving foreign genetic information, as it can be potentially dangerous if, for example, important genes are damaged by integration into its chromosome, resulting in major disadvantages for the organism as a whole . Therefore, bacteria have developed numerous mechanisms that protect them from absorbing harmful DNA. Many of the molecular processes involved were discovered in recent years, leading to the coining of the term “bacterial immune system”.

Now, a team from the Microbial Biochemistry and Cell Biology Group at the Institute of General Microbiology at the University of Kiel has elucidated the function of a new defense mechanism that can identify and, if necessary, break down several independent structures and mobile pieces of DNA called plasmids in bacteria. cells – distinguishing between useful and harmful genetic information.

Using the bacterium Corynebacterium glutamicum as an example, the researchers showed that the so-called Mks protein system has an additional element that can bind to plasmid DNA and cleave it. Kiel scientists led by Professor Marc Bramkamp published their new results in Nucleic Acids Research.

Proteins for organizing DNA can also protect against plasmids

Plasmids are small, usually circular, double-stranded DNA molecules that can replicate independently of the chromosome in their host cell. They play an important role in the ecology and evolution of bacteria, as they are an important means of lateral gene transfer, enabling the rapid transfer of genetic information and thus the expression of selection advantages. In principle, all bacteria can exchange plasmids with each other even across species.

This happens directly from bacterium to bacterium through a transfer mechanism known as conjugation. Favorable and unfavorable plasmids use such bridges between bacterial cells to pass from one bacterium to another.

“How the bacterial organism deals with foreign DNA from newly transferred plasmids has been little investigated until now,” Manuela Weiß, Ph.D. student in Bramkamp’s research group points out. “In previous research, we have investigated systems that are generally involved in the organization of DNA in bacterial cells and, among other things, ensure the packaging of genetic information in the compact form of chromosomes,” continues Weiß.

In this context, the research team received initial indications that C. glutamicum possesses two such systems, one of which is not involved in chromosome organization, but can prevent the multiplication of some plasmids, although the mechanism responsible for this was previously unknown. seen. .

Now, Kiel researchers, together with experts led by Dr. Anne Marie Wehenkel of the Institut Pasteur in Paris discovered the DNA scissors of the Mks system in a structural study. “We were able to prove experimentally that this new subunit of the Mks system forms a specific protein, a so-called nuclease, which can cut DNA. This element has the task of degrading plasmids in order to keep the DNA in the harmful away from the bacterial cell. , while the other components of the Mks system are important for the recognition of plasmid DNA”, says Weiß.

Distinguish between beneficial and harmful plasmids

The researchers then followed up with the observation that the Mks system apparently only degrades certain plasmids and that it must therefore be linked to a selection mechanism. An important advantage here is that Bramkamp’s research group is working with the bacterium C. glutamicum, an organism that naturally possesses this system. Therefore, its functions can be studied in vivo without changing the biological properties of cells by transferring it to a model system.

“Bacteria use certain plasmids as a source of new, not immediately vital, genetic information. It is therefore clear that a defense mechanism must be selective and not destroy all plasmids,” says Bramkamp.

“We were able to prove that in C. glutamicum there is indeed a selection directed at beneficial and harmful genetic information. When we artificially turned off the Mks system and thus all plasmids remained in the bacterial cells, the harmful effects on the cell, possibly caused by DNA stress, were evident. However, these did not occur when the defense mechanism was active,” continues Bramkamp.

With the current work, the Kiel researchers are presenting important new findings about the bacterial immune system in general, which expand the understanding of plasmids as mediators of not only beneficial but also harmful genetic information. In the future, they want to investigate which molecular mechanisms allow bacterial cells to distinguish between “good” and “bad” mobile DNA.

The new results are not only important for the general understanding of the organization and reproduction of bacterial life. Increasingly precise research of the bacterial immune system can also help to better meet applied challenges – and, for example, to better model and predict the evolution of antibiotic resistance in certain bacterial populations in the future.

More information: Manuela Weiß et al, The nuclease MksG is the executing part of the bacterial plasmid defense system MksBEFG, Nucleic Acids Research (2023). DOI: 10.1093/nar/gkad130

Journal Information: Nucleic Acids Research