Disrupting pathogens with RNAs


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Disrupting pathogens with RNAs

We’ve heard a lot about RNAs lately with RNA vaccines. But what are RNAs? RNA stands for Ribonucleic acid. In other words, they are nucleic acids like DNA, but with a ribose, a five-carbon sugar molecule. The RNA molecule you heard of lately is mRNA or messenger RNA. As its name implies, it’s a messenger that transfers the message from DNA by copying it and bringing it to ribosomes that will translate it into proteins with the help of tRNAs. For the vaccine, it’s a messenger that will tell our cells how to make the spike protein from SARS-CoV-2 so it can teach our immune system to recognize the virus when it sees it. 

mRNAs are not the only RNA molecules, there is also tRNA (transfer RNA discussed here), rRNA (part of the building block of ribosomes), snRNAs (small nuclear RNAs that are located in the nucleus), and other non-coding RNAs such as small RNAs (sRNAs) (Figure 1). 

Figure 1. Types of RNAs (biorender template)

Bacterial sRNAs are highly important as regulatory molecules. They usually bind to protein targets and modify their function, or they can also interact with mRNA which will regulate gene expression directly. They are therefore involved in many different mechanisms related to: 

  • Stress response
  • Regulation of RpoS (transcription regulator)
  • Regulation of outer membrane proteins
  • Pathogen virulence
  • Quorum sensing (bacterial communication system)
  • Biofilm formation
  • Antibiotic resistance

These regulatory mechanisms are therefore highly important in pathogenic bacteria. These bacteria regulate their gene expression to evade our immune system and cause disease. Using sRNA to regulate gene expression is a fast and energy-efficient way compared to more conventional transcription factors (which are proteins). Many regulatory RNAs have been studied, especially in pathogenic bacteria, but whether they take part in causing disease is still not well understood. 

In a recent study, a team developed a genetic system to study sRNAs and their impact on pathogenicity in the bacteria responsible for the cause of Chlamydia: Chlamydia trachomatis. Chlamydia are bacteria infecting our cells and causing different diseases. Chlamydia trachomatis is the most common cause of bacterial sexually transmitted disease, with more than 1.8 million new cases reported annually in the U.S. These bacteria can also cause infectious blindness called trachoma, while related species such as C. pneumoniae are responsible for pneumonia.

All Chlamydia spp. have a similar developmental cycle that alternates between two forms within a eukaryotic host cell. An infectious form, called the elementary body (EB in blue), binds and enters the host cell. After several hours, the EB differentiates into a larger, intracellular form, known as the reticulate body (RB in red), in a vacuole called inclusion. RBs are metabolically active and undergo multiple rounds of replication before converting back into EBs. This step is critical for transmission because only EBs can infect new host cells (Figure 2). 

Figure 2: Developmental cycle of Chlamydia species. https://commons.wikimedia.org/wiki/File:OSC_Microbio_04_02_Chlamydia.jpg

In this study, the authors screened thirteen chlamydial sRNAs for deleterious effects on the infection and identified several whose overexpression caused a severe reduction in infection. In particular, sRNA CtrR3 overexpression caused an RB-to-EB conversion defect (green sRNA, Figure 3). Therefore, EBs were not formed well and could not infect more cells. Another sRNA overexpression, CtrR7, caused an RB replication defect (blue sRNA, Figure 3). This time, RBs could not replicate efficiently reducing the amount of EBs produced and limiting infectiousness. 

Figure 3. The two sRNAs targeting RB cells. (From https://commons.wikimedia.org/wiki/File:OSC_Microbio_04_02_Chlamydia.jpg with Biorender and Canva)

They combined their genetic approach with biochemical, bioinformatic, mutational, and functional analyses to identify the target of these sRNAs. In this case, the targets were mRNAs involved in important development steps. This study is essential for future research in pathogens and opens a door to potential treatment areas. While sRNAs have been previously studied in model organisms such as E. coli, it is crucial that regulation after transcription in pathogens can also be studied in order to develop treatments in the future that would reduce the infectivity of the pathogen or its virulence to enable treatments to work more effectively or directly act as an antibiotic.

Link to the original post: Wang, K., Sheehan, L., Ramirez, C., Densi, A., Rizvi, S., Ekka, R., … Tan, M. (2022). A Reverse Genetic Approach for Studying sRNAs in Chlamydia trachomatis. MBio. https://doi.org/10.1128/mbio.00864-22‌

Featured image: Adapted from https://upload.wikimedia.org/wikipedia/commons/d/da/DNA_RNA_structure_%28full%29.png