Viruses Infecting a Freshwater Filamentous Cyanobacterium ( Nostoc sp.) Encode a Functional CRISPR Array and a Proteobacterial DNA Polymerase B

Abstract

Here we present the first genomic characterization of viruses infecting Nostoc, a genus of ecologically important cyanobacteria that are widespread in freshwater. Cyanophages A-1 and N-1 were isolated in the 1970s and infect Nostoc sp. strain PCC 7210 but remained genomically uncharacterized. Their 68,304- and 64,960-bp genomes are strikingly different from those of other sequenced cyanophages. Many putative genes that code for proteins with known functions are similar to those found in filamentous cyanobacteria, showing a long evolutionary history in their host. Cyanophage N-1 encodes a CRISPR array that is transcribed during infection and is similar to the DR5 family of CRISPRs commonly found in cyanobacteria. The presence of a host-related CRISPR array in a cyanophage suggests that the phage can transfer the CRISPR among related cyanobacteria and thereby provide resistance to infection with competing phages. Both viruses also encode a distinct DNA polymerase B that is closely related to those found in plasmids of Cyanothece sp. strain PCC 7424, Nostoc sp. strain PCC 7120, and Anabaena variabilis ATCC 29413. These polymerases form a distinct evolutionary group that is more closely related to DNA polymerases of proteobacteria than to those of other viruses. This suggests that the polymerase was acquired from a proteobacterium by an ancestral virus and transferred to the cyanobacterial plasmid. Many other open reading frames are similar to a prophage-like element in the genome of Nostoc sp. strain PCC 7524. The Nostoc cyanophages reveal a history of gene transfers between filamentous cyanobacteria and their viruses that have helped to forge the evolutionary trajectory of this previously unrecognized group of phages.

Integrated mobile genetic elements in Thaumarchaeota

“…The vast majority of known CRSIPR-Cas systems are encoded by cellular organisms and deployed to counter the replication of MGE, but some MGE also carry functional CRISPR-Cas systems. For instance, CRISPR-Cas systems and stand-alone CRISPR arrays have been identified in a number of prophages (Hargreaves et al, 2014;Chénard et al, 2016;Zheng et al, 2016;Garneau et al, 2018) and in the case of a Vibrio-infecting bacteriophage have been shown to target for destruction a pathogenicity island integrated in the host genome (Seed et al, 2013). By contrast, a subgroup of Tn7-like transposons has been hypothesized to employ the encoded CRISPR-Cas system for CRISPR-guided transposition (Peters et al, 2017).…”

Cylindrospermopsis raciborskii Virus and host: genomic characterization and ecological relevance

“…A CRISPR array has been reported in the genome cyanophage N‐1, a myovirus which infects Nostoc sp. PCC7210 (Chenard et al ., ). To our knowledge, this is the only other instance of a CRISPR being found in a cyanophage genome.…”

“…In contrast, the two viral CRISPRs were dissimilar in DR sequence. The DRs in N‐1 were similar to the DR5 family, which is common in cyanobacteria, and were most similar to those in filamentous cyanobacteria, indicating the likely source of the N‐1 array and providing additional evidence for the horizontal transfer of CRISPRs via viruses (Makarova et al ., ; Chenard et al ., ).…”

“…Amino acid sequence of the terminase large subunit protein (TerL) can be used to predict DNA packaging strategy (Casjens et al, 2005) and is commonly used to examine phylogeny of phages (Sullivan et al, 2009;Huang et al, 2012;Chenard et al, 2016). Placement of the CrV terminase sequence into a phylogenetic tree of sequences of phages whose DNA packaging strategies are known indicates that the CrV uses a T4-like headful packaging strategy and that the genome is circularly permuted (Supporting Information Fig.…”

“…However, processing by a host Cas system of CRISPR RNAs from prophage arrays has been demonstrated (Soutourina et al, 2013), setting up a straightforward and easy to visualize mechanism in which CRISPRs could afford a fitness advantage to the possessing prophage by influencing and perhaps preventing infections by other phage (Hargreaves et al, 2014). In the case of lytic viruses, use of the host Cas system to process viral CRISPR RNAs could potentially protect against co-infection (Chenard et al, 2016). Indeed, Chenard et al demonstrated that the N-1 CRISPR was transcribed during active infection and that the host contains a CRISPR-Cas system.…”