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Danish Archaea Centre, Department of Molecular Biology, Biocenter, Copenhagen University, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark
Correspondence
Xu Peng
peng{at}mermaid.molbio.ku.dk
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ABSTRACT |
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 TOP ABSTRACT INTRODUCTIONMETHODSRESULTS AND DISCUSSIONCONCLUDING REMARKSREFERENCES |
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The GenBank/EMBL/DDBJ accession numbers for the sequences of SSV4 and pXZ1 are EU030938 and EU030940, respectively.
Supplementary tables showing primers for amplification of Southern hybridization probes and for the PCR test of SSV4 integration, the properties of SSV4 ORFs and operons, and reannotated ORFs in the genomes of SSV2, SSV RH, SSV K1 and SSV1, are available with the online version of this paper.
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INTRODUCTION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONCONCLUDING REMARKSREFERENCES |
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; Lipps, 2007; Brügger et al., 2007). These genetic elements play important roles in the evolution of their host organisms and some have provided a basis for studying archaeal cellular processes and for developing archaeal genetic systems.
The Fuselloviridae is one of seven crenarchaeal viral families that have been classified recently. Four members (SSV1, SSV2, SSV K1 and SSV RH), all sharing the same morphology, i.e. a spindle shape with a short tail, have been isolated from widely different geographical locations. SSV1 (also known as SAV1) was identified in Sulfolobus shibatae from Beppu, Japan, as a plasmid and shown later on to be the episomal form of a novel UV-inducible virus (Martin et al., 1984). SSV2 was isolated from a Sulfolobus islandicus strain sampled from a solfataric hot spring in Reykjanes, Iceland (Stedman et al., 2003), while SSV K1 was from the Kamchatka region of Eastern Russia and SSV RH was isolated from Yellowstone National Park, USA (Wiedenheft et al., 2004). Each of these viruses can infect Sulfolobus solfataricus P2, which was isolated from Naples, Italy, indicating that they have a broader host range than other known crenarchaeal viruses (Prangishvili et al., 2006).
Each virus contains a circular dsDNA genome of about 15 kb with about 34 ORFs which show little or no similarity to sequences in public databases. However, comparative genome analyses of the four viruses have revealed that about one half of each genome is highly conserved while the other half is variable (Wiedenheft et al., 2004). Four gene products have been assigned functions: two viral coat proteins VP1 and VP3 which are shared between the viruses, another coat protein VP2 encoded only by SSV1, and a tyrosine integrase. The last facilitates recombination between the viral and archaeal attachment sites, attP and attA, respectively, producing a partitioned integrase gene upon integration into the host chromosome (Muskhelishvili et al., 1993; Serre et al., 2002).
Of particular interest is that SSV2 was isolated together with a satellite, pSSVx, which can spread through a Sulfolobus culture in the presence of a helper virus such as SSV1 or SSV2 (Arnold et al., 1999; Stedman et al., 2003). The plasmid–virus hybrid pSSVx is a fusion between a pRN-type plasmid and two genes originating from SSVs which were considered to be involved in the packaging of pSSVx (Arnold et al., 1999). Another virus satellite, pSSVi, was recently identified in S. solfataricus P2 cells, where it was present only in an integrated form. Upon transformation of the cells by SSV2 DNA prepared from S. islandicus REY31A, pSSVi was excised from the host genome and replicated actively (Wang et al., 2007). Like pSSVx, pSSVi can also be packaged into a spindle-like viral particle and spread with the help of SSV1 or SSV2. pSSVi resembles members of the pRN plasmid family in genome organization but encodes an SSV-type integrase (Wang et al., 2007). The conserved genome region of pSSVx and of the other pRN-type plasmids isolated from Iceland includes a replication protein RepA, a putative copy number-control protein CopG and a putative regulatory protein PlrA (Peng et al., 2000; Lipps, 2007). However, three pRN-type plasmids isolated from New Zealand carry similar copG and/or plrA genes but encode either a much less conserved RepA or a completely different replication protein (Greve et al., 2005). For example, the N-terminal sequence of RepA in pTIK4 shows no sequence similarity to the corresponding ORF regions of other pRN plasmids and the large ORF in pTAU4 encodes a putative minichromosome maintenance protein (MCM). Thus, the pRN plasmids constitute a diverse family. Although a few pRN-type elements have been discovered in an integrated form in the chromosomes of Sulfolobus (e.g. Peng et al., 2000), the only free form of a pRN-type plasmid encoding an integrase is the recently described plasmid–virus hybrid pSSVi (Wang et al., 2007).
The work presented here describes the co-isolation of a new member of the Fuselloviridae, SSV4, and an integrase-containing pRN-type plasmid, pXZ1, from a pure Sulfolobus strain. In contrast to pSSVx and pSSVi, pXZ1 did not spread together with SSV4. Genomic features of the two elements are described and their site-specific integration into host chromosomes is demonstrated.
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METHODS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONCONCLUDING REMARKSREFERENCES |
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). Single-colony clones were then isolated from 0.7 % Gelrite plates (Kelco) and inoculated into 50 ml medium. Cultures were then screened for plaque formation using S. solfataricus P2 as an indicator strain, as described by Schleper et al. (1992). Positive clones were further cultured in 250 ml medium and supernatants were investigated for the presence of virus-like particles by transmission electron microscopy (TEM), as described by Zillig et al. (1994). SSV4 was identified from a pure strain isolated from the enrichment S. islandicus ARN3 (collected from Arnavatn, Iceland). Since a few pure strains had already been isolated from the same enrichment (Prangishvili et al., 1998), this particular strain was designated S. islandicus ARN3/6.
Virus purification and DNA isolation.
Cells were isolated from cultures by centrifugation at 7000 g for 15 min at 4 °C, and extrachromosomal covalently closed circular (ccc)DNA was purified using Plasmid Miniprep and Maxiprep Kits (Qiagen). Virus particles were precipitated from culture supernatants by adding 1 M NaCl and 10 % (w/v) PEG 6000 (final concentrations) and stirred overnight at 4 °C. The precipitated virus was collected by centrifuging at 15 000 g for 30 min. Virus particles were purified by centrifugation at 69 000 g for 24 h at 20 °C in a CsCl density gradient (0.39 g ml–1). The virus band was removed and dialysed against 10 mM Tris/acetate buffer, pH 6, and stored at 4 °C. Nucleic acid was isolated from the purified virus as described by Zillig et al. (1994).
DNA analysis and sequencing.
DNAs were digested with the restriction enzyme BglII, and fragments were separated by agarose gel electrophoresis and visualized by staining with ethidium bromide or SYBR gold (Invitrogen). Shotgun libraries were constructed by inserting sonicated and end-repaired DNA fragments in the size range 1.5–4 kb into a pUC18 vector. Clones were sequenced in MegaBACE sequenators (Amersham Biotech) to yield a fivefold sequence coverage of the genomes. Contig assemblies were accomplished with Sequencher version 4.3 (Gene Codes). Any remaining gaps or ambiguous regions, including the highly similar integrase genes, were PCR-amplified, and the products were sequenced on both strands.
Sequence analyses.
ORFs were located and adjusted using putative TATA-like promoter motifs and Shine–Dalgarno (SD) motifs (Torarinsson et al., 2005) in the Artemis V9 program (Sanger Institute). Employing all three start codons (AUG, GUG and UUG), genes were defined by initially selecting for the largest possible ORFs. When the presence of TATA-like and/or SD motifs supported the existence of a shorter coding region, this was selected. BLASTP searches were performed against the EMBL/NCBI database (Altschul et al., 1997) and conserved protein domains were detected by MotifScan in ExPASy Proteomics Tools (http://www.expasy.org/tools/). Nucleotide sequence alignments between SSVs were accomplished by BLASTN searches against the Sulfolobus Database (Brügger, 2007).
Southern hybridization and PCR.
Total DNAs from S. islandicus ARN3/6 and virus-infected S. solfataricus P2 cells were extracted as described by Zillig et al. (1994). Total DNAs and extrachromosomal cccDNA isolated from S. islandicus ARN3/6 cells were digested with the restriction enzyme BglII and the resulting fragments were analysed by standard Southern blot hybridization procedures (Sambrook & Russell, 2001). DNA fragments upstream of the integrase gene in SSV4 and pXZ1 were PCR-amplified and labelled by DIG-11-dUTP, alkali-labile, with a Random Primed DNA Labeling Kit (Roche Applied Science). After hybridization, DIG-labelled DNA was detected by chemiluminescent CDP-Star (Roche Applied Science).
PCR was performed to confirm integration of SSV4 into the S. solfataricus P2 chromosome. The primers used in the experiment, as well as in generating probes for Southern hybridization analyses, were purchased from TAG Copenhagen. Sequences of PCR primers are available in Supplementary Table S1.
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RESULTS AND DISCUSSION |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONCONCLUDING REMARKSREFERENCES |
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). Consistent with this, most of the samples from the Zillig Iceland collection produced plaque-like haloes on cell lawns of S. solfataricus P2. In order to obtain pure virus-containing strains, single-colony clones were isolated from the enrichments and screened for the presence of viruses (see Methods).
Spindle-shaped virus particles were observed by TEM in the culture supernatant of a pure strain, S. islandicus ARN3/6, indicating the possible presence of an SSV-like virus (Fig. 1a). Moreover, the cell-free supernatant of the culture was able to produce clear plaques on cell lawns of S. solfataricus P2. In order to demonstrate infectivity of the putative virus, a Gelrite slice containing the plaque zone and the surrounding S. solfataricus P2 cells was inoculated into fresh medium. The supernatant of the late-exponential-phase culture was shown by TEM to contain spindle-shaped particles with a morphology identical to that observed from the original host (Fig. 1a). Moreover, viruses purified from the infected S. solfataricus P2 cells could also produce plaques on cell lawns of uninfected S. solfataricus P2 cells. This demonstrated that the spindle-shaped particles were indeed infectious virions. Subsequent sequencing showed that virions contained a dsDNA genome similar to those of the previously characterized members of the Fuselloviridae (see below). Therefore, the virus was named SSV4.
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). Four large fragments ranging from 2 to about 6.5 kb were produced from SSV4 genomic DNA, which correlated accurately with its genome sequence (see below). Moreover, a 5.5 kb fragment was found to be present at a higher molar ratio than the SSV4 bands (Fig. 1b, lane 1). However, DNA extracted from virions did not contain this fragment, nor did the extrachromosomal cccDNA or viral DNA prepared from infected S. solfataricus P2 cultures (Fig. 1b). This suggested that the DNA was not packaged into viral particles. The fragment was sequenced and shown to constitute a pRN-like plasmid which we named pXZ1. In more than 10 individual infectivity assays in which PCR and/or Southern hybridization experiments (see below) were employed to investigate the spread of the two elements, only SSV4 was found to spread in S. solfataricus P2. This confirmed that pXZ1 is a plasmid. SSV4 and pXZ1 were both stably maintained in S. islandicus ARN3/6. After more than 10 continuous transfers of the culture into fresh medium, both elements remained detectable. Moreover, each of 20 colonies isolated from the colony-purified S. islandicus ARN3/6 was found to contain both SSV4 and pXZ1 (data not shown). Copy-number fluctuation was observed for both SSV4 and pXZ1. In the first few cultures of S. islandicus ARN3/6, or when SSV4 was first introduced into S. solfataricus P2, their copy numbers were quite high, as judged from a high DNA yield from the plasmid purification and the clear restriction pattern of SSV4 and pXZ1 in the total DNA digest. However, the copy number of both elements fell after continuous transfers of the culture, or after long-term storage of the cell stock at –80 °C. The highest copy number observed was about 30 per cell, while the lowest was about two per cell for each element, as revealed by Southern hybridization studies (see below).
Genome organization and gene content of SSV4
In order to further characterize the two elements, their complete genomes were sequenced (see Methods). SSV4 virions contain a circular dsDNA genome of 15 135 bp with a G+C content of 38.5 %, similar to that of the previously characterized SSVs (Wiedenheft et al., 2004). Thirty-three ORFs were identified, ranging in size from 45 to 808 aa (Fig. 2). About 25 of the ORFs were preceded by putative SD motifs, while only 10 were preceded by putative TATA-like sequences, and eight exhibited downstream T-rich sequences which are likely to be transcriptional terminators (Reiter et al., 1988). More than half of the ORFs overlapped with adjacent genes, and 11 were located less than 20 bp from the next gene and were therefore considered to form part of an operon. The information on putative promoter and terminator sequences, as well as the distance between genes, is summarized in Supplementary Table S2. In total, four putative operons were identified that comprised 29 genes. All genes, except the first ones in the putative operons, exhibited SD motifs, whereas in general the single genes and the first genes of operons did not, as has been observed earlier for Sulfolobus and other archaeal genomes (Tolstrup et al., 2000; Torarinsson et al., 2005). The annotation of SSV4 operons is supported by the similar organization of the experimentally detected SSV1 co-transcripts (Fig. 2) (Reiter et al., 1987; Fröls et al., 2007).
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). For example, ORF A168 of SSV2 is 44 aa longer than the homologous ORF124 in SSV4 and 39 aa longer than ORF B129 of SSV1. ORF A168, which lacks an SD motif and was assigned a CUG start codon, was reannotated to ORF A168 (124) encoding 124 aa and carrying an AUG start codon and GGAGG SD motif (Fig. 2, Supplementary Table S3). Other ORFs were also re-examined for the presence of a putative TATA-like motif, an SD motif and/or terminator sequences in the earlier-characterized SSV genomes. This resulted in two to nine genes being reannotated in each viral genome (Fig. 2, Supplementary Table S3). Moreover, similar operon structures were predicted for the genomes of SSV2, SSV RH and SSV K1 (data not shown).
About 90 % of the start codons of SSV4 were AUG, and a few started at GUG or UUG, as found in the genomes of S. solfataricus and Sulfolobus tokodaii (Garcia-Vallve et al., 2003). However, in contrast to the Sulfolobus chromosomal genes that use the UAA stop codon in preference to UGA and UAG, more than 60 % of SSV4 ORFs terminated at UGA (Table 1). This is also true for the other SSVs, which average 50–60 % UGA, but is not true for the other crenarchaeal viruses, which average 20–30 % UGA (Table 1). Further analysis revealed that about three-quarters of the UGA stop codons in SSVs were part of the SD motif of a next gene (GGTGA), or overlapped by 1 (TGATG) or 4 bp (ATGA) with the start codon of the following ORF. This demonstrated that SSV genomes are organized in a highly compact fashion, whereby the TGA sequence can be multifunctional.
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, Table 2). It is noteworthy that the putative transcription regulators are concentrated in the genomic region corresponding to the two early transcription units T5 and T6 identified for SSV1, which are considered to be responsible for genome replication (Fröls et al., 2007; Fig. 2). This suggests that the putative transcription regulators are involved in the regulation of genome replication through protein–protein and/or protein–DNA interactions.
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, Table 3). ORFs 82 and 52 show high similarities to pRN putative regulatory protein (PlrA) and copy number control protein (CopG), respectively, while ORF75 shows a similarity to pDL ORF72, which is located immediately upstream of repA and has been designated CopG-like (Kletzin et al., 1999). Homologues of the latter have also been found at the same genomic region of pSSVx and of two integrated pRN elements in Sulfolobus chromosomes, pST1 and pXQ1 (She et al., 2007). Although ORF1077 showed limited similarity to the putative RepA protein of pTIK4 and a bacterial DNA primase-like protein (Table 3), no recognizable protein domain was detected. This suggests that ORF1077 constitutes a novel type of replication protein. Previous sequence comparison has shown that pRN plasmids isolated from Iceland have very similar replication proteins, whereas those from Italy and New Zealand encode quite different RepAs (reviewed by Lipps, 2007). The presence of a distantly related putative replication protein in the novel pRN plasmid isolated from Iceland, pXZ1, reinforces the diversity of the replication proteins of pRN plasmids.
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; Wang et al., 2007), ORF129 yields no sequence matches in public databases and ORF76 shows similarity only in a 30 aa region to ORF90a of pRN1.
Based on high sequence similarities to integrase genes encoded in the SSV genomes (Table 3), ORF 331 from pXZ1 was annotated as an integrase-encoding gene. The amino acid sequence identity/similarity between ORF331 and its closest homologue, the SSV4 integrase gene, is 86/94 %. Given that pXZ1 was co-isolated with SSV4 from a single-colony culture and that the two elements are stably maintained in the same host, the high similarity strongly suggests that ORF331 originated from SSV4.
Although a few integrase-containing pRN-type elements have been found in Sulfolobus chromosomes (Peng et al., 2000; She et al., 2007), none of the eight previously characterized extrachromosomal pRN plasmids contains an integrase gene (reviewed by Lipps, 2007). Only the recently identified virus satellite pSSVi, originally present in an integrated form in an S. solfataricus strain and excised upon introduction of SSV2 DNA into the host cells, is similar to pRN plasmids in genome organization; it encodes an integrase which shows only 38/57 % amino acid identity/similarity to that of SSV2 (Wang et al., 2007). This raises the question of the origin of the integrase genes present in the integrated pRN-like elements. The identification of the pXZ1 integrase gene provides the first strong evidence that it was probably transferred from an SSV.
The genome maps of pXZ1, pSSVi and pSSVx, together with that of pRN1 (Keeling et al., 1998), are aligned in Fig. 3. A common feature shared between the first three is that they coexist with an SSV and each shares homologous genes with SSVs which may be of viral origin. While pXZ1 and pSSVi encode SSV-type integrases, pSSVx contains two genes that are conserved in SSVs (Fig. 3). Thus, co-existing with an SSV in the same host apparently facilitates the uptake of viral genes into the pRN genomes, which may confer a survivial advantage upon the latter by enabling integration into host chromosomes or packaging into viral particles and hence spreading together with the virus. Unlike pSSVi and pSSVx, however, pXZ1 remains as a plasmid and does not spread with SSV4 to other host cells. This could be due to the absence of a packaging signal in the genome of pXZ1.
Integration of SSV4 and pXZ1
The presence of a putative integrase gene in the genomes of SSV4 and pXZ1 suggests that they are capable of integrating into host chromosomes. To test this possibility, Southern hybridization experiments were performed. Firstly, their putative attachment sites (attP) were identified and aligned with the putative attA sites in the genome of S. solfataricus P2 (Sso) (She et al., 2001). As shown in Fig. 4(a), the attP sequences of SSV4 and pXZ1 match perfectly with the 3' halves of the genes for tRNAGlu[UUC] and tRNAGlu[CUC], respectively. Except for one mismatch in the anticodon (UUC vs CUC), the two tRNA genes are identical in the genome of S. solfataricus P2, including their intron sequences (She et al., 2001). tRNA genes with sequences identical to those of S. solfataricus tRNAGlu[UUC] and tRNAGlu[CUC] also occur in the genome of S. islandicus HVE10/4 (K. Brügger and others, unpublished results), which was isolated from Iceland and is closely related to S. islandicus ARN3/6 (Zillig et al., 1994). Given the close relationship between the two S. islandicus strains, the same two tRNA genes are expected to be present in the natural host strain of SSV4 and pXZ1.
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). A fragment of 1.6 kb was detected in addition to the two episomal fragments in total DNA from the virus-infected S. solfataricus P2, consistent with the expected 1635 bp host–SSV4 hybrid band assuming tRNAGlu[UUC] to be the attachment site (Fig. 4b, lanes 2 and 2'). An extra band of 4.2 kb was also detected from the total DNA of S. islandicus ARN3/6 (Fig. 4b, lane 1). Although the complete genome sequence is unavailable, the size matches closely with the predicted 4252 bp assuming that tRNAGlu[UUC] in the chromosome of S. islandicus HVE 10/4 is the attachment site (K. Brügger and others, unpublished results). This suggests a high sequence similarity between the two S. islandicus strains. In order to verify the integration, PCR experiments were employed to amplify the border of the virus–host hybrid from total DNA of virus-infected S. solfataricus P2 (Fig. 4d). Subsequent sequencing of the PCR products confirmed the integration of SSV4 into tRNAGlu[UUC].
Hybridization with a pXZ1-specific probe revealed one band in addition to the episomal fragment from S. islandicus ARN3/6 total DNA (Fig. 4c), indicating that pXZ1 integrated into one site in the host chromosome. Estimating from the genome sequence of S. islandicus HVE 10/4 that is available in our laboratory (K. Brügger and others, unpublished results), integration into tRNAGlu[CUC] would produce a host–pXZ1 hybrid fragment of 3388 bp after BglII digestion, whereas a 5101 bp fragment would be expected after integration into tRNAGlu[UUC]. Therefore, the presence of a 3.4 kb hybrid fragment strongly indicates a site-specific integration of pXZ1 into the tRNAGlu[CUC] gene (Fig. 4c). As expected, neither the episomal nor the integrated form of pXZ1 was detected in the virus-infected S. solfataricus P2 total DNA (Fig. 4c, lane 2). This confirms that pXZ1 is a plasmid and does not spread together with SSV4 in a foreign host.
As mentioned above, the integrase gene encoded in pXZ1 probably derived from SSV4, and this is consistent with the 88 % overall nucleotide identity between the two genes. About 500 bp in the centre, including the attP site, are almost identical. The only mismatch within this region is found at a position corresponding to the mutated nucleotide in the anticodon of the two tRNA genes (Fig. 4a). Thus, this single point mutation seems to have been positively selected and has conferred on pXZ1 the ability to integrate into a different tRNA gene from that targeted by SSV4, thereby avoiding any competition for integration sites.
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CONCLUDING REMARKS |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONCONCLUDING REMARKSREFERENCES |
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), the role of their site-specific integration has rarely been interpreted in terms of their own requirements but rather in terms of the advantages for host genome evolution (She et al., 2007). Given the harsh and destructive environment that most known crenarchaea and their viruses encounter, site-specific integration, at least for viruses with circular genomes, is probably advantageous for virus survival. Thus, taking over and modifying the viral integrase to create a new plasmid integration site in the host chromosome provides an alternative strategy for enhancing plasmid survival. This suggests that plasmids use different strategies to survive in Sulfolobus cells growing under extreme conditions. When coexisting with a fusellovirus either they exploit the viral integrase, as described here, to integrate into a different chromosomal site or they exploit the viral packaging system and spread as a virus satellite, as found for pSSVx and pSSVi.
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ACKNOWLEDGEMENTS |
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Edited by: J. van der Oost
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REFERENCES |
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TOPABSTRACTINTRODUCTIONMETHODSRESULTS AND DISCUSSIONCONCLUDING REMARKSREFERENCES |
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Arnold, H. P., She, Q., Phan, H., Stedman, K., Prangishvili, D., Holz, I., Kristjansson, J. K., Garrett, R. & Zillig, W. (1999). The genetic element pSSVx of the extremely thermophilic crenarchaeon Sulfolobus is a hybrid between a plasmid and a virus. Mol Microbiol 34, 217–226.[CrossRef][Medline]
Brügger, K. (2007). The Sulfolobus database. Nucleic Acids Res 35, (Database issue), D413–D415.[CrossRef][Medline]
Brügger, K., Peng, X. & Garrett, R. A. (2007). Sulfolobus genomes: mechanisms of rearrangement and change. In Archaea: Evolution, Physiology and Molecular Biology, pp. 95–104. Edited by R. A. Garrett & H. P. Klenk. Oxford: Blackwell.
Fröls, S., Gordon, P. M., Panlilio, M. A., Schleper, C. & Sensen, C. W. (2007). Elucidating the transcription cycle of the UV-inducible hyperthermophilic archaeal virus SSV1 by DNA microarrays. Virology 365, 48–59.[CrossRef][Medline]
Garcia-Vallve, S., Guzman, E., Montero, M. A. & Romeu, A. (2003). HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes. Nucleic Acids Res 31, 187–189.
Greve, B., Jensen, S., Phan, H., Brügger, K., Zillig, W., She, Q. & Garrett, R. A. (2005). Novel RepA-MCM proteins encoded in plasmids pTAU4, pORA1 and pTIK4 from Sulfolobus neozealandicus. Archaea 1, 319–325.[Medline]
Keeling, P. J., Klenk, H. P., Singh, R. K., Schenk, M. E., Sensen, C. W., Zillig, W. & Doolittle, W. F. (1998). Sulfolobus islandicus plasmids pRN1 and pRN2 share distant but common evolutionary ancestry. Extremophiles 2, 391–393.[CrossRef][Medline]
Kletzin, A., Lieke, A., Urich, T., Charlebois, R. L. & Sensen, C. W. (1999). Molecular analysis of pDL10 from Acidianus ambivalens reveals a family of related plasmids from extremely thermophilic and acidophilic archaea. Genetics 152, 1307–1314.
Lipps, G. (2007). Plasmids. In Archaea: Evolution, Physiology and Molecular Biology, pp. 105–112. Edited by R. A. Garrett & H. P. Klenk. Oxford: Blackwell.
Martin, A., Yeats, S., Janekovic, D., Reiter, W. D., Aicher, W. & Zillig, W. (1984). SAV 1, a temperate u.v.-inducible DNA virus-like particle from the archaebacterium Sulfolobus acidocaldarius isolate B12. EMBO J 3, 2165–2168.[Medline]
Muskhelishvili, G., Palm, P. & Zillig, W. (1993). SSV1-encoded site-specific recombination system in Sulfolobus shibatae. Mol Gen Genet 237, 334–342.[CrossRef][Medline]
Palm, P., Schleper, C., Grampp, B., Yeats, S., McWilliam, P., Reiter, W. D. & Zillig, W. (1991). Complete nucleotide sequence of the virus SSV1 of the archaebacterium Sulfolobus shibatae. Virology 185, 242–250.[CrossRef][Medline]
Peng, X., Holz, I., Zillig, W., Garrett, R. A. & She, Q. (2000). Evolution of the family of pRN plasmids and their integrase-mediated insertion into the chromosome of the crenarchaeon Sulfolobus solfataricus. J Mol Biol 303, 449–454.[CrossRef][Medline]
Prangishvili, D., Albers, S. V., Holz, I., Arnold, H. P., Stedman, K., Klein, T., Singh, H., Hiort, J., Schweier, A. & other authors (1998). Conjugation in Archaea: frequent occurrence of conjugative plasmids in Sulfolobus. Plasmid 40, 190–202.[CrossRef][Medline]
Prangishvili, D., Forterre, P. & Garrett, R. A. (2006). Viruses of the Archaea: a unifying view. Nat Rev Microbiol 4, 837–848.[CrossRef][Medline]
Reiter, W. D., Palm, P. & Zillig, W. (1987). Gene expression in archaebacteria: physical mapping of constitutive and UV-inducible transcripts from the Sulfolobus virus-like particle SSV1. Mol Gen Genet 209, 270–275.[CrossRef][Medline]
Reiter, W. D., Palm, P. & Zillig, W. (1988). Transcription termination in the archaebacterium Sulfolobus: signal structures and linkage to transcription initiation. Nucleic Acids Res 16, 2445–2459.
Sambrook, J. & Russell, D. J. (2001). Molecular Cloning, a Laboratory Manual, 3rd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory.
Schleper, C., Kubo, K. & Zillig, W. (1992). The particle SSV1 from the extremely thermophilic archaeon Sulfolobus is a virus: demonstration of infectivity and of transfection with viral DNA. Proc Natl Acad Sci U S A 89, 7645–7649.
Serre, M. C., Letzelter, C., Garel, J. R. & Duguet, M. (2002). Cleavage properties of an archaeal site-specific recombinase, the SSV1 integrase. J Biol Chem 277, 16758–16767.
She, Q., Singh, R. K., Confalonieri, F., Zivanovic, Y., Allard, G., Awayez, M. J., Chan-Weiher, C. C., Clausen, I. G., Curtis, B. A. & other authors (2001). The complete genome of the crenarchaeon Sulfolobus solfataricus P2. Proc Natl Acad Sci U S A 98, 7835–7840.
She, Q., Zhu, H. & Xiang, X. (2007). Integration mechanisms: possible role in genome evolution. In Archaea: Evolution, Physiology and Molecular Biology, pp. 113–124. Edited by R. A. Garrett & H. P. Klenk. Oxford: Blackwell.
Stedman, K. M., She, Q., Phan, H., Arnold, H. P., Holz, I., Garrett, R. A. & Zillig, W. (2003). Relationships between fuselloviruses infecting the extremely thermophilic archaeon Sulfolobus: SSV1 and SSV2. Res Microbiol 154, 295–302.[Medline]
Tolstrup, N., Sensen, C. W., Garrett, R. A. & Clausen, I. G. (2000). Two different and highly organized mechanisms of translation initiation in the archaeon Sulfolobus solfataricus. Extremophiles 4, 175–179.[CrossRef][Medline]
Torarinsson, E., Klenk, H.-P. & Garrett, R. A. (2005). Divergent transcriptional and translational signals in Archaea. Environ Microbiol 7, 47–54.[CrossRef][Medline]
Wang, Y., Duan, Z., Zhu, H., Guo, X., Wang, Z., Zhou, J., She, Q. & Huang, L. (2007). A novel Sulfolobus non-conjugative extrachromosomal genetic element capable of integration into the host genome and spreading in the presence of a fusellovirus. Virology 363, 124–133.[CrossRef][Medline]
Wiedenheft, B., Stedman, K., Roberto, F., Willits, D., Gleske, A.-K., Zoeller, L., Snyder, J., Douglas, T. & Young, M. (2004). Comparative genomic analysis of hyperthermophilic archaeal fuselloviridae viruses. J Virol 78, 1954–1961.
Zillig, W., Kletzin, A., Schleper, C., Holz, I., Janecovik, D., Hain, J., Lanzendorfer, M. & Kristjansson, J. (1994). Screening for Sulfolobales, their plasmids and viruses in Icelandic solfataras. Syst Appl Microbiol 16, 609–628.
Received 5 September 2007;
revised 30 October 2007;
accepted 1 November 2007.
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