Investigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans

Abstract

CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. S. mutans strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and ‘openness’ of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.

Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Streptococcus mutans

“…Notably, we have recently discovered that S. mutans strains carry CRISPR spacers against this element [46]. This finding suggests that S.…”

“…To begin to understand whether TnSmu1 is capable of conjugative transfer, we wanted to determine whether closely and distantly related strains of S. mutans carry this ICE. Notably, we have recently discovered that S. mutans strains carry CRISPR spacers against this element [ 46 ]. This finding suggests that S. mutans strains encounter TnSmu1, or genes from related ICEs, and CRISPR-Cas is recording these horizontal transfer events.…”

Human saliva modifies growth, biofilm architecture, and competitive behaviors of oral streptococci

“…Other upregulated genes of note included the glucosyltransferases gtfBC (SMU.1004, SMU.1005), the bacitracin resistance ABC transporters mbrAB (SMU.1006-SMU.1007) ( 36 ), and the TnSmu2 gene cluster which contains genes for mutanobactin synthesis ( 37 ). In contrast, many of the downregulated genes (74 DEGs) belonged to the integrative and conjugative element TnSmu1 ( 38 , 39 ), the genetic competence regulon ( 40 ), a CRISPR2-Cas system ( 41 , 42 ), and predicted amino acid ABC transporters (SMU.932–SMU.936). Interestingly, the most downregulated genes within the data set belonged to the trehalose-specific PTS ( 43 , 44 ).…”

Activation of TnSmu1, an integrative and conjugative element, by an ImmR-like transcriptional regulator in Streptococcus mutans

“…To begin to understand if TnSmu1 is capable of conjugative transfer, we wanted to determine if closely and distantly related strains of S. mutans carry this ICE. Notably, we have recently discovered that S. mutans strains carry CRISPR spacers against this element [35]. This finding suggests that S. mutans attempts to prevent transfer/acquisition of TnSmu1 via CRISPR-Cas mediated immunity, and it also provides evidence of potential transfer between strains.…”