Genetic Diversity and Evolution

Sulfolobus tengchongensis Spindle-Shaped Virus STSV1: Virus-Host Interactions and Genomic Features

Xiaoyu Xiang, Lanming Chen, Xiaoxing Huang, Yuanmin Luo, Qunxin She, Li Huang
DOI: 10.1128/JVI.79.14.8677-8686.2005

Article Figures & Data

Figures

  • FIG. 1.
    FIG. 1.

    Transmission electron micrographs of STSV1. Upper left panel, virus particles (bars, 200 nm); other panels, virus particles attached to S. tengchongensis RT8-4 cells (bars, 1 μm).

  • FIG. 2.
    FIG. 2.

    Thin-layer chromatography of lipids extracted from STSV1 particles and uninfected S. tengchongensis RT8-4 cells. The arrows indicate bands that occur differently in the two samples.

  • FIG. 3.
    FIG. 3.

    Analysis of proteins in the STSV1 virion. Purified STSV1 particles were subjected to SDS-polyacrylamide gel (12%) electrophoresis. After electrophoresis, the gel was stained with Coomassie brilliant blue R-250. The proteins in the bands were sliced and subjected to in-gel digestion with trypsin and identified by determining the masses of the tryptic peptides by two-dimensional chromatography coupled with ion trap mass spectrometry. ORFs encoding the proteins are indicated on the right, and molecular size standards (in kDa) are on the left.

  • FIG. 4.
    FIG. 4.

    Infection of S. tengchongensis RT8-4 by STSV1. The titer of STSV1 in the extracellular fluid, determined using a plaque assay, represents the highest dilution at which the sample was capable of forming plaques. The viral DNA associated with the host cells was quantitated by dot blotting. Symbols: □; cell density of an RT8-4 culture infected with STSV1; ▴, cell-associated viral DNA; ▵, virus titer in the extracellular fluid.

  • FIG. 5.
    FIG. 5.

    Restriction analysis of DNAs isolated from STSV1 particles, uninfected S. tengchongensis RT8-4 cells, and RT8-4 cells infected with STSV1. DNAs were isolated from virus particles and infected or uninfected cells and digested with EcoRI. The digests were electrophoresed in 0.8% agarose. Lane 1, size markers (from top to bottom: 10, 8, 6, 5, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.75, 0.5 and 0.25 kb); lane 2, purified STSV1 DNA; lane 3, DNA from uninfected RT8-4 cells; lane 4, DNA from RT8-4 cells infected with STSV1.

  • FIG. 6.
    FIG. 6.

    Southern blotting analysis of the restriction fragments of STSV1 DNA isolated from virus particles and S. tengchongensis RT8-4 cells infected with STSV1. Purified STSV1 DNA (lanes 1 and 3) and total DNA from RT8-4 cells infected with STSV1 (lanes 2 and 4) were digested with EcoRV, and the restriction digests were separated by electrophoresis in 0.8% agarose. Hybridization was performed using radiolabeled total viral DNA (left panel) or an int-containing fragment (right panel) as a probe.

  • FIG. 7.
    FIG. 7.

    Modification of STSV1 DNA. Purified STSV1 DNA and total DNAs from uninfected S. tengchongensis RT8-4 cells and from RT8-4 cells infected with STSV1 were digested with different restriction endonucleases and separated in 1% agarose gels. Lanes 1, 4, 14, and 19, size markers (from top to bottom: 10, 8, 6, 5, 4, 3.5, 3, 2.5, 2, 1.5, 1, 0.75, 0.5 and 0.25 kb); lane 2, STSV1 DNA digested with XhoI; lane 3, STSV1 DNA digested with PstI; lane 5, RT8-4 DNA digested with PstI; lane 6, DNA from infected RT8-4 cells digested with PstI; lane 7, STSV1 DNA digested with PstI; lane 8, RT8-4 DNA digested with MspI; lane 9, RT8-4 DNA digested with HpaII; lane 10, DNA from infected RT8-4 cells digested with MspI; lane 11, DNA from infected RT8-4 cells digested with HpaII; lane 12, STSV1 DNA digested with MspI; lane 13, STSV1 DNA digested with HpaII; lane 15, undigested STSV1 DNA; lane 16, STSV1 DNA digested with DpnI; lane 17, STSV1 DNA digested with Sau3AI; lane 18, STSV1 DNA digested with MboI.

  • FIG. 8.
    FIG. 8.

    Organization of the STSV1 genome. Putative ORFs are shown as arrows along the line representing the genome. ORFs encoding putative enzymes or proteins are indicated in black, and those resembling hypothetical ORFs from Sulfolobus species or their viruses are in grey.

  • FIG. 9.
    FIG. 9.

    Cumulative GC skew of the STSV1 genome. The putative origin of viral DNA replication is indicated by an arrow.

  • FIG. 10.
    FIG. 10.

    Sequence features of the region containing the putative origin of STSV1 DNA replication. The positions of the cis elements in the region and the start codon of ORF1 are numbered with reference to the complete sequence of STSV1. (A) An illustration of the putative replication origin. TR1, tandem repeat 1; TR2, tandem repeat 2; loop1, stem-loop 1; loop2, stem-loop 2. The figure was not drawn to scale. (B) Sequence alignment of the 25-bp tandem repeats (TR1). Bases conserved in at least three repeats are highlighted in black. The consensus sequence is shown at the bottom. (C) Inverted repeats forming stem-loop structures. Mismatches are in lowercase letters. (D) Multiple sequence alignment of the 40-bp tandem repeats.

Additional Files

  • HTML Page - index.htslp

    Files in this Data Supplement:

    • Supplemental file 1 - Table S1. Sequence features of ORFs in the STSV1 genome.
      MS Word document, 147K.
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