A Novel Cyanophage with a Cyanobacterial Nonbleaching Protein A Gene in the Genome

Abstract

A cyanophage, PaV-LD, has been isolated from harmful filamentous cyanobacterium Planktothrix agardhii in Lake Donghu, a shallow freshwater lake in China. Here, we present the cyanophage's genomic organization and major structural proteins. The genome is a 95,299-bp-long, linear double-stranded DNA and contains 142 potential genes. BLAST searches revealed 29 proteins of known function in cyanophages, cyanobacteria, or bacteria. Thirteen major structural proteins ranging in size from 27 kDa to 172 kDa were identified by SDS-PAGE and mass-spectrometric analysis. The genome lacks major genes that are necessary to the tail structure, and the tailless PaV-LD has been confirmed by an electron microscopy comparison with other tail cyanophages and phages. Phylogenetic analysis of the major capsid proteins also reveals an independent branch of PaV-LD that is quite different from other known tail cyanophages and phages. Moreover, the unique genome carries a nonbleaching protein A (NblA) gene (open reading frame [ORF] 022L), which is present in all phycobilisome-containing organisms and mediates phycobilisome degradation. Western blot detection confirmed that 022L was expressed after PaV-LD infection in the host filamentous cyanobacterium. In addition, its appearance was companied by a significant decline of phycocyanobilin content and a color change of the cyanobacterial cells from blue-green to yellow-green. The biological function of PaV-LD nblA was further confirmed by expression in a model cyanobacterium via an integration platform, by spectroscopic analysis and electron microscopy observation. The data indicate that PaV-LD is an exceptional cyanophage of filamentous cyanobacteria, and this novel cyanophage will also provide us with a new vision of the cyanophage-host interactions. Cyanophages are one kind of planktonic viruses that infect cyanobacteria (blue-green algae). Cyanophages and phages have amazing amounts of genetic diversity and biological activity in water environments (33,34,40,54). In either a freshwater or saltwater environment, cyanophages are ubiquitous and play an important role in water ecosystems (46,52,61,66). Generally, the complete genome sequences of cyanophages can provide significant clues for better understanding of the biological properties, ecological effects, and coevolutionary relationships between cyanophages and their hosts (10,17,18,21,27,29). Some cyanophage genomes have been sequenced (32,35,44,49,51,60,64), which has revealed the presence of cyanobacterial genes involved in central energy metabolism and their host's survival. For examples, some photosynthesis-related genes (psbA, hliP, and PSII) and stress-response genes (coding for chaperones and genes associated with bacterial motility and chemotaxis) have been described in cyanophages (4, 5, 31, 36, 47), most of which are transcribed together with essential cyanophage replication-related genes (6, 13, 30, 65). Moreover, a nonbleaching protein A (NblA) gene has been found from a lytic phage, Ma-LMM01, infecting Microcystis aerugi...

Assessment of a metaviromic dataset generated from nearshore Lake Michigan

“…Further investigation showed that nearly all of these matches (Fig. 5a) were to the gene PaVLD_ORF033R, which is annotated as an ABCtransporter protein (Gao et al 2012). The presumptive abundance of this gene in our samples is extremely unlikely to represent a single 'species' of phage only, and is more likely owing to the high presence of non-species or virus-specific ABC-transporter proteins (ubiquitous throughout all extant prokaryotic and eukaryotic phyla alike) in the sample.…”

“…5a) were to the gene PaVLD_ORF033R. This protein is annotated as an ABC-transporter protein (Gao et al 2012) in RefSeq. Fig.…”

Polar freshwater cyanophage S-EIV1 represents a new widespread evolutionary lineage of phages

“…The detection of only six structural proteins for a phage of this size is undoubtedly an underestimation, especially given the complexity of the tail structure of S-EIV1. For example, SDS-PAGE analysis for cyanophage PaV-LD, which is about 80 nm in diameter and lacks a tail, resolved 13 structural proteins (Gao et al, 2012), while 14 structural proteins were resolved for Cyanophage Syn5 (Raytcheva et al, 2011). Ultimately, a mass spectrometry-based proteomics analysis would be a more sensitive approach for elucidating the structural proteins that make up the S-EIV1 virion.…”

“…Of the five sequenced cyanophages that infect Microcystis aeruginosa (Yoshida et al, 2008), Phormidium foveolarum (Liu et al, 2007(Liu et al, , 2008, Planktothrix agardhii (Gao et al, 2012) and Synechococcus spp. (Dreher et al, 2011), only the myovirus S-CRM01 that infects the latter is related to myoviruses infecting marine Synechococcus spp.…”

Unraveling the genome structure of cyanobacterial podovirus A-4L with long direct terminal repeats

“…Since the first total genome sequence of a Synechococcus cyanophage P60 was reported in 2002, more than 40 cyanophages from different species of cyanobacteria have been characterized at the genome level (Chen and Lu, 2002;Liu et al, 2008;Huang et al, 2012;Dreher et al, 2011;Gao et al, 2012;Labrie et al, 2013). Furthermore, some cyanophages have been reported to contain special genes, such as photosynthesis-related genes, carbon metabolism genes and phosphate stress genes, and these genes are speculated to play defining functional roles in cyanobacterial virus-host interactions (Lindell et al, 2004(Lindell et al, , 2005Sullivan et al, 2005;Gao et al, 2012). However, it is still limited to obtain sufficient evidence in support of such a speculation due to lack of well-characterized hosts that are readily amenable to genetic modification in these cyanobacterial virus-host systems.…”