Bioinformatic survey of CRISPR loci across 15 Serratia species

Abstract

The Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins (CRISPR-Cas) system of prokaryotes is an adaptative immune defense mechanism to protect themselves from invading genetic elements (e.g., phages and plasmids). Studies that describe the genetic organization of these prokaryotic systems have mainly reported on the Enterobacteriaceae family (now reorganized within the order of Enterobacterales). For some genera, data on CRISPR-Cas systems remain poor, as in the case of Serratia (now part of the Yersiniaceae family) where data are limited to a few genomes of the species marcescens. This study describes the detection, in silico, of CRISPR loci in 146 Serratia complete genomes and 336 high-quality assemblies available for the species ficaria, fonticola, grimesii, inhibens, liquefaciens, marcescens, nematodiphila, odorifera, oryzae, plymuthica, proteomaculans, quinivorans, rubidaea, symbiotica, and ureilytica. Apart from subtypes I-E and I-F1 which had previously been identified in marcescens, we report that of I-C and the I-E unique locus 1, I-E*, and I-F1 unique locus 1. Analysis of the genomic contexts for CRISPR loci revealed mdtN-phnP as the region mostly shared (grimesii, inhibens, marcescens, nematodiphila, plymuthica, rubidaea, and Serratia sp.). Three new contexts detected in genomes of rubidaea and fonticola (puu genes-mnmA) and rubidaea (osmE-soxG and ampC-yebZ) were also found. The plasmid and/or phage origin of spacers was also established.

Keywords: CRISPR system; RPW; Rhynchophorus ferrugineus; subtype I-C; subtype I-E; subtype I-F1.

Figure 1

Schematic diagram of the three categories of arrays described in the study. DRs and spacers are depicted with diamonds and rectangles respectively. cas genes are shown as arrows pointing in the direction of transcription. The yellow color highlights the consistency between the DR type and the cas subtype; while the blue color indicates inconsistency.

Figure 2

Architectures of canonical and unique cas gene sets. Genes are shown as arrows pointing in the direction of transcription. Gray shadows highlight the distinguishing features of the I‐E unique locus 1, I‐E*, and I‐F1 unique locus 1. Species in which the architectures were detected are reported on the right side and the number of genomes is reported in brackets. Truncated cas gene sets (due to the end of contigs) were not shown. (a) Genetic organization of the canonical cas gene set I‐C. (b) Genetic organization of cas gene sets for the canonical I‐E, the I‐E*, and I‐E unique locus 1. The WYL domain is highlighted as a red arrow. (c) Genetic organization of cas gene sets for the canonical I‐F1 and the I‐F1 unique locus 1.

Figure 3

Distribution of CRISPR‐positive genomes. Solid boxes represent the total number (top of boxes) of genomes analyzed per species. Dashed boxes show the number (top of boxes) of genomes for which CRISPR–Cas systems or CRISPRs were detected.

Figure 4

Cas3 phylogenetic tree. Species are shown with different colors. In brackets, the accession number of the cas3 nucleotide sequence is reported.

Figure 5

16S rRNA gene phylogenetic tree. Species are shown with different colors. In brackets, the accession number of the 16S rRNA gene nucleotide sequence is reported.

Figure 6

Schematic diagram of the shared genomic contexts A to D. Letters on the left (a–d) indicate the type of genomic context. The pink dashed box represents the genomic region harboring cas set and/or CRISPR arrays. Black thick lines depict flanking regions. Genes are shown as arrow boxes pointing in the direction of transcription.