CRISPR-Cas systems in multicellular cyanobacteria

Abstract

Novel CRISPR-Cas systems possess substantial potential for genome editing and manipulation of gene expression. The types and numbers of CRISPR-Cas systems vary substantially between different organisms. Some filamentous cyanobacteria harbor > 40 different putative CRISPR repeat-spacer cassettes, while the number of cas gene instances is much lower. Here we addressed the types and diversity of CRISPR-Cas systems and of CRISPR-like repeat-spacer arrays in 171 publicly available genomes of multicellular cyanobacteria. The number of 1328 repeat-spacer arrays exceeded the total of 391 encoded Cas1 proteins suggesting a tendency for fragmentation or the involvement of alternative adaptation factors. The model cyanobacterium Anabaena sp. PCC 7120 contains only three cas1 genes but hosts three Class 1, possibly one Class 2 and five orphan repeat-spacer arrays, all of which exhibit crRNA-typical expression patterns suggesting active transcription, maturation and incorporation into CRISPR complexes. The CRISPR-Cas system within the element interrupting the Anabaena sp. PCC 7120 fdxN gene, as well as analogous arrangements in other strains, occupy the genetic elements that become excised during the differentiation-related programmed site-specific recombination. This fact indicates the propensity of these elements for the integration of CRISPR-cas systems and points to a previously not recognized connection. The gene all3613 resembling a possible Class 2 effector protein is linked to a short repeat-spacer array and a single tRNA gene, similar to its homologs in other cyanobacteria. The diversity and presence of numerous CRISPR-Cas systems in DNA elements that are programmed for homologous recombination make filamentous cyanobacteria a prolific resource for their study. Abbreviations: Cas: CRISPR associated sequences; CRISPR: Clustered Regularly Interspaced Short Palindromic Repeats; C2c: Class 2 candidate; SDR: small dispersed repeat; TSS: transcriptional start site; UTR: untranslated region.

Keywords: CRISPR; cyanobacteria; heterocyst; nitrogen fixation; programmed DNA recombination.

Figure 1.

Phylogenetic analysis of 391 Cas1 sequences from 171 filamentous cyanobacteria. The three Cas1 protein sequences from Synechocystis sp. PCC 6803 were included in this unrooted phylogenetic tree, each representing a Cas1 cluster (grey shaded clusters) of 7 major clusters. Dark blue branches within light blue shaded clusters represent Cas1 proteins fused with a Cas4 domain, while red branches within light pink shaded clusters represent Cas1 proteins fused with a RV_1 domain. The positions of Cas1 proteins from Anabaena 7120 are given in brackets. The detailed Cas1 tree with sequence names and bootstrap values is presented in Figure S1, the protein sequences can be found in Supplemental Dataset 1.

Figure 2.

CRISPR-Cas systems and repeat-spacer arrays in three representative species, (A) Nostoc sp. PCC 7107, (B) Calothrix sp. PCC 7507 and (C) Rivularia sp. PCC 7116. The location of cas1 genes is indicated by asterisks, an added ‘RT_1’ or ‘1_4’ indicates RT or Cas4 fusions. Pseudogenes are labelled by a Φ symbol.

Figure 3.

Examples of CRISPR-Cas systems that are encoded on genetic elements that are excised during cell differentiation into nitrogen-fixing heterocysts. The upper example is in the model organism Anabaena 7120, in which a CRISPR-Cas system is present within the fdxN element. The gene alr1468 encoding a reverse transcriptase-Cas1 fusion protein is annotated; details for the repeat spacer arrays CR_2 and CR_3 can be found in Table 2. The lower example presents the nifK element in Calothrix desertica sp. PCC 7102. CRISPR repeat-spacer arrays are labelled ‘CRISPR’. Note that the Anabaena 7120 element contains a cas1-RT fusion gene that is framed by split instances of the repeat-spacer arrays CR_2 and CR_3. Recombinase genes are labeled xis and xisAFHI and colored purple, cas genes are colored red, genes related to nitrogen fixation are colored blue, all other genes are in grey.

Figure 4.

CRISPR-Cas systems in Anabaena 7120. Left: Alignments of CRISPR direct repeats. Right: Schematic distribution of CRISPR-cas systems, their subtype annotation and the location of repeat-spacer arrays in the chromosome of Anabaena 7120. The location of cas1 genes is indicated by asterisks and the respective gene IDs. For further details, see also Table 2.

Figure 5.

Expression of crRNAs from repeat-spacer arrays in Anabaena 7120. Total RNA was isolated from cultures grown under standard conditions for 8, 24 and 32 h after the removal of nitrogen, separated by electrophoresis on denaturing 15% PAA gels and transferred to nylon membranes. Single-stranded specific RNA probes were used for Northern hybridization. A control hybridization against 5S rRNA was performed to control for equal loading (the following membranes were  used twice: for CR_3 was re-hybridized with the CR_11 probe, CR_1 with the CR_2 and CR_4 with the CR_6 probe  later). The size of marker fragments is given on the left.

Figure 6.

Synteny of Class 2 candidate systems. On the left the phylogenetic relationships are drawn based on 16S rRNA sequences, on the right the arrangements of putative CRISPR-cas systems are depicted that have an all3613 homolog next to the array and lack any known genes for adaptation or other known cas gene. Note the frequent presence of different tRNA genes adjacent to the repeat-spacer arrays. The units consisting of the all3613 homolog, the repeat-spacer array and tRNA gene (if present) are boxed. Known and putative cas genes are colored orange. The different tRNA genes are colored in light green and shaded in yellow for visualization, and their cognate amino acid is indicated. Numbers on the phylogenetic tree are bootstrap values and given if ≥ 60. The position of the model Anabaena 7120 is highlighted by larger fonts. 16S rDNA sequence from Gloeobacter violaceus PCC7421 was used as an outgroup to root this tree.