Comparison of genome sequences of single-stranded RNA viruses infecting the bivalve-killing dinoflagellate Heterocapsa circularisquama - PubMed (original) (raw)

Comparison of genome sequences of single-stranded RNA viruses infecting the bivalve-killing dinoflagellate Heterocapsa circularisquama

Keizo Nagasaki et al. Appl Environ Microbiol. 2005 Dec.

Abstract

Heterocapsa circularisquama RNA virus (HcRNAV) has at least two ecotypes (types UA and CY) that have intraspecies host specificities which are complementary to each other. We determined the complete genomic RNA sequence of two typical HcRNAV strains, HcRNAV34 and HcRNAV109, one of each ecotype. The nucleotide sequences of the viruses were 97.0% similar, and each had two open reading frames (ORFs), ORF-1 coding for a putative polyprotein having protease and RNA-dependent RNA polymerase (RdRp) domains and ORF-2 encoding a single major capsid protein. Phylogenetic analysis of the RdRp amino acid sequence suggested that HcRNAV belongs to a new previously unrecognized virus group. Four regions in ORF-2 had amino acid substitutions when HcRNAV34 was compared to HcRNAV109. We used a reverse transcription-nested PCR system to amplify the corresponding regions and also examined RNAs purified from six other HcRNAV strains with known host ranges. We also looked at natural marine sediment samples. Phylogenetic dendrograms for the amplicons correlated with the intraspecies host specificities of the test virus strains. The cloned sequences found in sediment also exhibited considerable similarities to either the UA-type or CY-type sequence. The tertiary structure of the capsid proteins predicted using computer modeling indicated that many of the amino acid substitutions were located in regions on the outside of the viral capsid proteins. This strongly suggests that the intraspecies host specificity of HcRNAV is determined by nanostructures on the virus surface that may affect binding to suitable host cells. Our study shows that capsid alterations can change the phytoplankton-virus (host-parasite) interactions in marine systems.

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Figures

FIG. 1.

FIG. 1.

Genome of HcRNAV. (A) Schematic genome structure of HcRNAV34 and HcRNAV109 and the positions of the primers. Note the variable regions in ORF-2 correspond to those shown in Fig. 5. (B) Possible secondary structure for the 3′-terminal 49 nucleotides of HcRNAV34 and HcRNAV109.

FIG. 2.

FIG. 2.

Phylogenetic tree calculated from confidently aligned regions of amino acid sequences of RNA-dependent RNA polymerase alleles. The numbers at the nodes are bootstrap values (percentages) based on 1,000 samples. Nodes with bootstrap values less than 70% were collapsed. Scale bar = 0.5 fixed mutation per amino acid position. CABYV, cucurbit aphid-borne yellows virus; BChV, beet chlorosis virus; PEMV-1, pea enation mosaic virus 1; BYDV, barley yellow dwarf virus; PnLV, Poinsettia latent virus; MBV, mushroom bacilliform virus; RGMoV, ryegrass mottle virus; RYMV, rice yellow mottle virus; LTSV, lucerne transient streak virus; BoCV, bovine enteric calicivirus; NV, Norwalk virus; RHDV, rabbit hemorrhagic disease virus; PV, human poliovirus; BPMV, bean pod mottle virus; CPSMV, cowpea severe mosaic virus; RTSV, rice tungro spherical virus; PYFV, parsnip yellow fleck virus; SBV, sacbrood virus; DWV, deformed wing virus; TSV, Taura syndrome virus; DCV, Drosophila C virus; CrPV, cricket paralysis virus.

FIG. 3.

FIG. 3.

Phylogenetic tree calculated from confidently aligned regions of amino acid sequences encoded by the major capsid protein gene (ORF-2) fragments. A total of 245 amino acid sites were used to construct the tree. The numbers at the nodes are bootstrap values (percentages) based on 1,000 samples. Nodes with bootstrap values less than 70% were collapsed. Scale bar = 0.1 fixed mutation per amino acid position.

FIG. 4.

FIG. 4.

Tertiary structures of the major capsid proteins of HcRNAV34 (A to C) and HcRNAV109 (D to F) predicted by computer modeling. Three monomers that make up the capsid trimers are indicated by different colors (green, blue, and yellow), and the amino acid molecules where complete substitution was observed between the UA type and the CY type are indicated by red. (A and D) Surface side view; (B and E) reverse side view; (C and F) side view.

FIG. 5.

FIG. 5.

Amino acid alignment of the major capsid protein gene fragments of virus strains (four type UA HcRNAV strains and four type CY HcRNAV strains). Highly variable regions (regions I to IV) are highlighted. The asterisks indicate the amino acid positions at which complete substitution was observed between the UA type and the CY type for the eight strains tested.

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