Ma-LMM01 infecting toxic Microcystis aeruginosa illuminates diverse cyanophage genome strategies

Abstract

Cyanobacteria and their phages are significant microbial components of the freshwater and marine environments. We identified a lytic phage, Ma-LMM01, infecting Microcystis aeruginosa, a cyanobacterium that forms toxic blooms on the surfaces of freshwater lakes. Here, we describe the first sequenced freshwater cyanomyovirus genome of Ma-LMM01. The linear, circularly permuted, and terminally redundant genome has 162,109 bp and contains 184 predicted protein-coding genes and two tRNA genes. The genome exhibits no colinearity with previously sequenced genomes of cyanomyoviruses or other Myoviridae. The majority of the predicted genes have no detectable homologues in the databases. These findings indicate that Ma-LMM01 is a member of a new lineage of the Myoviridae family. The genome lacks homologues for the photosynthetic genes that are prevalent in marine cyanophages. However, it has a homologue of nblA, which is essential for the degradation of the major cyanobacteria light-harvesting complex, the phycobilisomes. The genome codes for a site-specific recombinase and two prophage antirepressors, suggesting that it has the capacity to integrate into the host genome. Ma-LMM01 possesses six genes, including three coding for transposases, that are highly similar to homologues found in cyanobacteria, suggesting that recent gene transfers have occurred between Ma-LMM01 and its host. We propose that the Ma-LMM01 NblA homologue possibly reduces the absorption of excess light energy and confers benefits to the phage living in surface waters. This phage genome study suggests that light is central in the phage-cyanobacterium relationships where the viruses use diverse genetic strategies to control their host's photosynthesis.

FIG. 1.

Ma-LMM01 genome organization. Red and blue arrows indicate putative ORFs. Pale blue and pink lines inside the circle show G+C and A+T contents, respectively.

FIG. 2.

Genomic dot plots for five cyanomyoviruses and T4. Dots correspond to high-scoring segments (>150 bp in length) detected by TBLASTX (i.e., translated query against translated target) with an E value threshold of 10⁻⁵.

FIG. 3.

Proportions of ORFs with database homologues for large DNA viruses. (Top) A total of 139 viruses with genomes larger than 100 kbp. Filled and open circles correspond to 28 phages and 111 eukaryotic viruses, respectively. (Bottom) Magnified view for the viruses with the smallest proportions of ORFs with homologues. For the identification of homologues, we used a BLAST E value of 10⁻⁵, excluding self matches. Note that for viral genomes with closely related genomes represented in the databases, the proportions of ORFs with database homologues become large.

FIG. 4.

Sequence alignment of NblA homologues. PCC7120, Nostoc sp. (Chr, chromosome [accession no. BAB76216]; PD, plasmid Delta [BAB77423]); PCC7937, Ananbaena variabilis (ABA22990); PCC73102, Nostoc punctiforme (ZP00345234); BP-1, Thermosynechococcus elongates (NP680824); PCC7601, Tolypothrix sp. strain PCC7601 (CAD28153); PCC6803, Synechocystis sp. (1, BAA17955; 2, BAA17954); PCC7942, Synechococcus sp. (ABB58157); PORPU, Porphyra purpurea (NP053976); AGLNE, Aglaothamnion neglectum (P48446); CYACA, Cyanidium caldarium (NP045072); CYAME, Cyanidoschyzon merolae (BAC76137). Conserved residues among the NblAs are shown in boxes (6). Amino acid residues binding to the PBS are marked with asterisks (6).

FIG. 5.

Transcription analysis of an intervening region between the DNA polymerase and 3′-5′exonuclease genes of Ma-LMM01. PCR targeting a 671-bp sequence between primer pairs at the 3′ end of ORF180 and 5′ end of ORF178 was performed using the following templates: lane 1, cDNA from host cells infected by Ma-LMM01; lane 2, DNase-treated RNA from host cells infected by Ma-LMM01; lane 3, DNA from Ma-LMM01.