A pooled CRISPRi screen to identify new cell cycle proteins in the opportunistic human pathogen Streptococcus pneumoniae

Project Information

GetToKnowPneumo

Grant agreement ID: 837923

DOI

10.3030/837923

Project closed

EC signature date 21 March 2019

Start date 1 April 2019

End date 31 March 2021

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 191 149,44

EU contribution

€ 191 149,44

Coordinated by

UNIVERSITE DE LAUSANNE
Switzerland

Periodic Reporting for period 1 - GetToKnowPneumo (A pooled CRISPRi screen to identify new cell cycle proteins in the opportunistic human pathogen Streptococcus pneumoniae)

Reporting period: 2019-04-01 to 2021-03-31

Summary of the context and overall objectives of the project

Streptococcus pneumoniae is an opportunistic human pathogen that is responsible for diseases such as pneumonia, middle ear infections, sepsis and meningitis and is an important cause of fatal bacterial infections. Moreover, antibiotic resistant S. pneumoniae strains are on the rise, thereby limiting effective treatment options. For these reasons, we set out to gain a better understanding of the cell biology of S. pneumoniae. Such increased knowledge not only has great fundamental scientific value, but could also be exploited in the design and development of novel antibacterial therapies.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

Using an innovative, genome-wide, pooled CRISPRi screening approach coupled to sorting of cells that display a phenotype of interest, we have identified genes involved in the regulation of S. pneumoniae cell size, DNA content and cell division, features that are important markers for cell cycle progression. This screen identified several targets that interfere with these processes, including genes of unknown and/or seemingly unrelated function. Our results therefore contribute towards a better understanding of these processes. Moreover, initial tests have shown the potential of some of these hits for the development of novel antibacterial therapies, which will be pursued further in the future.

Results will be disseminated shortly through publication of a scientific manuscript. Moreover, a potential patent application for novel antibacterial therapies is being prepared.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Although several bacterial genome-wide CRISPRi screens have been performed so far, none of these screen designs included the sorting of cells that display a phenotype of interest. By combining CRISPRi with high-throughput selection of desired phenotypes, we go beyond the state of the art and expand the use of pooled genome-wide CRISPRi screens beyond the investigation of fitness effects, as is current practice.

Moreover, our screen allowed us to identify a role for genes of unknown function in maintenance of S. pneumoniae cell size, DNA content and/or cell division, thereby further increasing our knowledge of these processes and genes.

Finally, we believe to have identified novel drug targets that could form the basis of innovative antibacterial therapies that are effective against S. pneumoniae. Follow-up work will explore these targets further and will hopefully result in the development of novel treatment options.

Overview of our CRISPRi-FACS-seq screen