Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

Carver, Tim; Berriman, Matthew; Tivey, Adrian; Patel, Chinmay; Böhme, Ulrike; Barrell, Barclay G.; Parkhill, Julian; Rajandream, Marie‐Adèle

doi:10.1093/bioinformatics/btn529

Cited by 534 publications

(513 citation statements)

References 6 publications

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“…The annotated contigs, containing CDS and RNA gene predictions, were submitted to the RAST online service for functional annotation (Aziz et al, 2008). The annotations were curated using the Artemis software suite (Carver et al, 2008). The annotated sequences were deposited at the European Nucleotide Archive (accession numbers CCNS01000001-CCNS01000139).…”

Section: Proteome Analysismentioning

confidence: 99%

Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Stopnišek¹,

Zühlke²,

Carlier³

et al. 2015

The ISME Journal

101

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Bacterial species belonging to the genus Burkholderia have been repeatedly reported to be associated with fungi but the extent and specificity of these associations in soils remain undetermined. To assess whether associations between Burkholderia and fungi are widespread in soils, we performed a co-occurrence analysis in an intercontinental soil sample collection. This revealed that Burkholderia significantly co-occurred with a wide range of fungi. To analyse the molecular basis of the interaction, we selected two model fungi frequently co-occurring with Burkholderia, Alternaria alternata and Fusarium solani, and analysed the proteome changes caused by cultivation with either fungus in the widespread soil inhabitant B. glathei, whose genome we sequenced. Co-cultivation with both fungi led to very similar changes in the B. glathei proteome. Our results indicate that B. glathei significantly benefits from the interaction, which is exemplified by a lower abundance of several starvation factors that were highly expressed in pure culture. However, co-cultivation also gave rise to stress factors, as indicated by the increased expression of multidrug efflux pumps and proteins involved in oxidative stress response. Our data suggest that the ability of Burkholderia to establish a close association with fungi mainly lies in the capacities to utilize fungalsecreted metabolites and to overcome fungal defense mechanisms. This work indicates that beneficial interactions with fungi might contribute to the survival strategy of Burkholderia species in environments with sub-optimal conditions, including acidic soils.

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Section: Proteome Analysismentioning

confidence: 99%

Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Stopnišek¹,

Zühlke²,

Carlier³

et al. 2015

The ISME Journal

101

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“…The obtained phage nucleotide sequences were analysed using Clone Manager (Sci-Ed8) and Artemis software (Carver et al, 2008). The phage sequences within the draft genome were identified using PHAge Search Tool (PHAST) (Zhou et al, 2011).…”

mentioning

confidence: 99%

Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 – characterization of their genomes, proteomes and DNA methyltransferases

Dziewit

Radlińska

2016

Journal of General Virology

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Aeromonas species are causative agents of a wide spectrum of diseases in animals and humans. Although these bacteria are commonly found in various environments, little is known about their phages. Thus far, only one temperate Aeromonas phage has been characterized. Whole-genome sequencing of an Aeromonas sp. strain ARM81 revealed the presence of two prophage clusters. One of them is integrated into the chromosome and the other was maintained as an extrachromosomal, linear plasmid-like prophage encoding a protelomerase. Both prophages were artificially and spontaneously inducible. We separately isolated both phages and compared their genomes with other known viruses. The novel phages show no similarity to the previously characterized Aeromonas phages and might represent new evolutionary lineages of viruses infecting Aeromonadaceae. Apart from the comparative genomic analyses of these phages, complemented with their structural and molecular characterization, a functional analysis of four DNA methyltransferases encoded by these viruses was conducted. One of the investigated N6-adenine-modifying enzymes shares sequence specificity with a Dam-like methyltransferase of its bacterial host, while another one is non-specific, as it catalyzes adenine methylation in various sequence contexts. The presented results shed new light on the diversity of Aeromonas temperate phages.

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“…Genomic sequences of other S. pyogenes strains used for comparative purposes were obtained from the NCBI Database, with RefSeq accession NC_003485 for M18-MGAS8232 and NC_009332 for M5-Manfredo. Genomic comparisons were performed using the BLAST (Zhang et al, 2000) and MUMmer (Delcher et al, 2002) and graphically viewed with Mauve (Darling et al, 2004) and ACT (Carver et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

Novel genomic rearrangements mediated by multiple genetic elements in Streptococcus pyogenes M23ND confer potential for evolutionary persistence

et al. 2016

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Symmetric genomic rearrangements around replication axes in genomes are commonly observed in prokaryotic genomes, including Group A Streptococcus (GAS). However, asymmetric rearrangements are rare. Our previous studies showed that the hypervirulent invasive GAS strain, M23ND, containing an inactivated transcriptional regulator system, covRS, exhibits unique extensive asymmetric rearrangements, which reconstructed a genomic structure distinct from other GAS genomes. In the current investigation, we identified the rearrangement events and examined the genetic consequences and evolutionary implications underlying the rearrangements. By comparison with a close phylogenetic relative, M18-MGAS8232, we propose a molecular model wherein a series of asymmetric rearrangements have occurred in M23ND, involving translocations, inversions and integrations mediated by multiple factors, viz., rRNA-comX (factor for late competence), transposons and phage-encoded gene segments. Assessments of the cumulative gene orientations and GC skews reveal that the asymmetric genomic rearrangements did not affect the general genomic integrity of the organism. However, functional distributions reveal re-clustering of a broad set of CovRS-regulated actively transcribed genes, including virulence factors and metabolic genes, to the same leading strand, with high confidence (p-value~10 À10 ). The re-clustering of the genes suggests a potential selection advantage for the spatial proximity to the transcription complexes, which may contain the global transcriptional regulator, CovRS, and other RNA polymerases. Their proximities allow for efficient transcription of the genes required for growth, virulence and persistence. A new paradigm of survival strategies of GAS strains is provided through multiple genomic rearrangements, while, at the same time, maintaining genomic integrity.

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Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

Cited by 534 publications

References 6 publications

Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Molecular mechanisms underlying the close association between soil Burkholderia and fungi

Two novel temperate bacteriophages co-existing in Aeromonas sp. ARM81 – characterization of their genomes, proteomes and DNA methyltransferases

Novel genomic rearrangements mediated by multiple genetic elements in Streptococcus pyogenes M23ND confer potential for evolutionary persistence

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