Investigating the relationship between CRISPR-Cas content and growth rate in bacteria

Abstract

CRISPR-Cas systems provide adaptive immunity for prokaryotic cells by recognizing and eliminating the recurrent genetic invaders whose sequences had been captured in a prior infection and stored in the CRISPR arrays as spacers. However, the biological factors determining the efficiency of this adaptive immune system have not been fully characterized. Recent studies in cultured bacteria showed that slowing the growth rate of bacterial cells could promote their acquisition of novel spacers. This paper reports a positive correlation between the minimal doubling time and the spacer abundance across the bacteria domain. The correlation is still significant after controlling for the effect of growth temperature. This observation provides evidence for the existence of the trade-off between bacterial growth and defense proposed in the "Killing the Winner" hypothesis.

Bacterial defenses and their trade-off with growth are not ubiquitous but depend on ecological contexts

“…Due to its smaller sample size, we opted not to utilize the dataset of prokaryotic empirical minimal doubling times provided by Madin et al (2020) in this study. While empirical data typically offer higher accuracy compared to computationally generated predictions, predictive methodologies have their own advantages (Liu et al 2023). Empirical minimal doubling periods may offer superior advantages over computationally generated predictions due to the inherent limitations of predictive methodologies achieving 100% precision.…”

“…Similarly, Abi systems are sporadically distributed across bacterial phylogeny (Stern and Sorek 2011), while RM systems are widespread but absent in about 4% of bacterial genomes (Roberts et al 2015). Additionally, the uneven distribution of antiviral defense systems extends to the archaeal lineage (Roberts et al 2015; Makarova et al 2020), reflecting trade-offs between the costs of maintaining such systems and the benefits gained in phage resistance (Winter et al 2010; Ferenci 2016; Pančić and Kiørboe 2018; Rostøl and Marraffini 2019; Thingstad 2022; Liu et al 2023).…”

“…Recently, we conducted an investigation into the relationship between growth rate and adaptive immunity in 4142 bacteria, utilizing predicted minimal doubling times retrieved from the EGGO database and CRISPR-Cas systems annotated with CRISPRCasFinder (Couvin et al 2018; Weissman et al 2021; Liu et al 2023). Our findings unveiled a significant positive correlation, indicating evolutionary trade-offs between growth and adaptive defense against virulent phages within the bacterial domain.…”

“…To gain a comprehensive understanding of the trade-off between prokaryotic growth and defense, investigations encompassing diverse environments and species are essential. Recent research analyzing growth rates and adaptive immunity across bacterial domains revealed a significant positive correlation, indicating evolutionary trade-offs between growth and adaptive defense against virulent phages (Liu et al, 2023). Additionally, besides CRISPR-Cas systems, prokaryotes possess numerous other antiviral mechanisms, such as the RM and Abi systems, warranting further exploration (Koonin et al, 2017;Bernheim and Sorek, 2020;Georjon and Bernheim, 2023;Tesson and Bernheim, 2023).…”

“…Similarly, Abi systems are sporadically distributed across bacterial phylogeny (7), while RM systems are widespread but absent in about 4% of bacterial genomes (10). Additionally, the uneven distribution of antiviral defense systems extends to the archaeal lineage (9,10), reflecting trade-offs between the costs of maintaining such systems and the benefits gained in phage resistance (8,(11)(12)(13)(14)(15).…”