Spiroplasma citri Virus SpV1: Characterization of Viral Sequences Present in the Spiroplasmal Host Chromosome

Bébéar, C.; Aullo, P.; Bové, J.M.; Renaudin, Joël

doi:10.1007/s002849900024

Cited by 31 publications

(16 citation statements)

References 22 publications

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“…Because several plectroviral insertion sites are shared among strains within S. citri (Bébéar et al 1996) and within S. melliferum (Alexeev et al 2012; Lo et al 2013), these plectroviral fragments are assumed to be inheritable. However, between-species comparisons indicate that few insertion sites are shared between S. citri and S. melliferum (fig.…”

Section: Resultsmentioning

confidence: 99%

“…melliferum are not overwhelmed by viral fragments and have not attained such large sizes, it implies that losses of viral fragments are also taking place at a comparable rate to counteract viral invasion. The removal of these repetitive sequences may be partially driven by the intrinsic deletional bias in bacteria that maintains their genome compactness (Kuo and Ochman 2009), as indicated by the presence of truncated viral genes (Carle et al 2010) and partial viral fragments (Bébéar et al 1996). …”

Section: Resultsmentioning

confidence: 99%

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Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma

Chen

et al. 2013

Genome Biology and Evolution

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Spiroplasma is a genus of wall-less, low-GC, Gram-positive bacteria with helical morphology. As commensals or pathogens of plants, insects, ticks, or crustaceans, they are closely related with mycoplasmas and form a monophyletic group (Spiroplasma–Entomoplasmataceae–Mycoides) with Mycoplasma mycoides and its relatives. In this study, we report the complete genome sequences of Spiroplasma chrysopicola and S. syrphidicola from the Chrysopicola clade. These species form the sister group to the Citri clade, which includes several well-known pathogenic spiroplasmas. Surprisingly, these two newly available genomes from the Chrysopicola clade contain no plectroviral genes, which were found to be highly repetitive in the previously sequenced genomes from the Citri clade. Based on the genome alignment and patterns of GC-skew, these two Chrysopicola genomes appear to be relatively stable, rather than being highly rearranged as those from the Citri clade. Phylogenetic analyses suggest that the susceptibility to plectroviral invasion probably originated in the common ancestor of the Citri clade or one of its subclades. This susceptibility may be attributed to the absence of antiviral systems found in the Chrysopicola clade. Using the virus-free genomes of the Chrysopicola clade as references, we inferred the putative viral integration sites in the Citri genomes. Comparisons of syntenic regions suggest that the extensive viral invasion in the Citri clade promoted genome rearrangements and expansions. More importantly, the viral invasion may have facilitated horizontal gene transfers that contributed to adaptation in the Citri clade.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma

Chen

et al. 2013

Genome Biology and Evolution

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“…A partial sequence was available for a fourth, the L10 element. Of the six sequences, only one, that of the L10 element, lacks major deletions relative to SpVl viral DNA (Bébéar et al, 1996). To obtain clues as to how these aberrant sequences arose, insertion and deletion junctions ( Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Indeed, the approximately 1.6 Mbp genomes of each of more than 20 tested S. citri strains contain multiple dispersed sequences related to parts of SpVl genomes (Bébéar et al, 1996). Considerable interstrain variation in the pattern of viral probe-reactive fragments was noted.…”

Section: Introductionmentioning

confidence: 99%

Mechanisms of Spiroplasma Genome Variation Associated with SpVl-like Viral DNA Inferred from Sequence Comparisons

Melcher¹,

Sha²,

Ye³

et al. 1999

Microbial & Comparative Genomics

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Genomes of Spiroplasma citri strains have rearranged frequently during their evolution, partly due to multiple integrated sequences of spiroplasma viruses. To understand better the role of viral sequences in genome evolution, we examined available nucleotide sequences of viruslike elements in the S. citri chromosome. Comparison of integrated and nonintegrated sequences of spiroplasma virus SpV1-C74 DNA suggested that it is an encapsidated form of the circular transposition intermediate belonging to an insertion sequence (IS3) family member. One SpV1-C74 viral DNA fragment was identified as interrupting the remains of a DNA adenine modification methylase gene. A viral DNA insertion of SpV1-R8A2 B DNA had hallmarks of having suffered an internal deletion by a site-specific recombination system. Homologous recombination likely was responsible for several deletions within viral DNA. A homologous recombination event was inferred between part of a viral DNA insertion and a similar chromosomal sequence. Dispersed sequences from SpV1-like C4 open reading frames (ORFs) were identified as involved in a complex deletion-inversion event. Thus, SpV1-like sequences likely have altered spiroplasma genomes by inserting within active genes, destroying their function, by providing targets for site-specific recombination, by mediating deletions of sequences adjacent to their integration sites, and by providing targets for homologous recombination, leading to inversions.

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“…In S. citri, the chromosome sizes vary from 1.6 to 1.9 Mbp among strains (53,54), and part of the size variation is thought to result from different amounts of prophage sequences (35). Many S. citri strains are infected by single-stranded DNAcontaining filamentous phages (Plectrovirus), whose sequences also occur as partial or full-length prophages integrated into the spiroplasma chromosome (7,35,38). Here we report the partial chromosome sequence of S. citri strain GII3-3X and the functional assignment of the predicted coding sequences.…”

mentioning

confidence: 99%

Partial Chromosome Sequence of Spiroplasma citri Reveals Extensive Viral Invasion and Important Gene Decay

Carle

Saillard

Carrère

et al. 2010

Appl Environ Microbiol

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The assembly of 20,000 sequencing reads obtained from shotgun and chromosome-specific libraries of the Spiroplasma citri genome yielded 77 chromosomal contigs totaling 1,674 kbp (92%) of the 1,820-kbp chromosome. The largest chromosomal contigs were positioned on the physical and genetic maps constructed from pulsed-field gel electrophoresis and Southern blot hybridizations. Thirty-eight contigs were annotated, resulting in 1,908 predicted coding sequences (CDS) representing an overall coding density of only 74%. Cellular processes, cell metabolism, and structural-element CDS account for 29% of the coding capacity, CDS of external origin such as viruses and mobile elements account for 24% of the coding capacity, and CDS of unknown function account for 47% of the coding capacity. Among these, 21% of the CDS group into 63 paralog families. The organization of these paralogs into conserved blocks suggests that they represent potential mobile units. Phage-related sequences were particularly abundant and include plectrovirus SpV1 and SVGII3 and lambda-like SpV2 sequences. Sixty-nine copies of transposases belonging to four insertion sequence (IS) families (IS30, IS481, IS3, and ISNCY) were detected. Similarity analyses showed that 21% of chromosomal CDS were truncated compared to their bacterial orthologs. Transmembrane domains, including signal peptides, were predicted for 599 CDS, of which 58 were putative lipoproteins. S. citri has a Sec-dependent protein export pathway. Eighty-four CDS were assigned to transport, such as phosphoenolpyruvate phosphotransferase systems (PTS), the ATP binding cassette (ABC), and other transporters. Besides glycolytic and ATP synthesis pathways, it is noteworthy that S. citri possesses a nearly complete pathway for the biosynthesis of a terpenoid.

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Spiroplasma citri Virus SpV1: Characterization of Viral Sequences Present in the Spiroplasmal Host Chromosome

Cited by 31 publications

References 22 publications

Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma

Complete Genomes of Two Dipteran-Associated Spiroplasmas Provided Insights into the Origin, Dynamics, and Impacts of Viral Invasion in Spiroplasma

Mechanisms of Spiroplasma Genome Variation Associated with SpVl-like Viral DNA Inferred from Sequence Comparisons

Partial Chromosome Sequence of Spiroplasma citri Reveals Extensive Viral Invasion and Important Gene Decay

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