Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities

Mantri, Yogita; Williams, Kelly P.

doi:10.1093/nar/gkh059

Cited by 102 publications

(99 citation statements)

References 20 publications

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“…Four of the 17 SARs showed the hallmark pattern of genomic islands, flanked on one side by an intact tRNA gene and on the other side by a fragment of that tRNA gene. Three of these, 8T (SAR 1-2), 15G (SAR 1-7), and 2I (SAR 1-12), have been described previously in chromosome 1 (36), and we identified a novel genomic island; SAR 2-10 is found in chromosome 2 and is 14 kb in length. This island is integrated into a tRNAThr and contains a type I restriction-modification system.…”

Section: Resultsmentioning

confidence: 68%

“…Finally, SARs were cross-referenced with previously published studies. Several of these interrupt a tRNA gene and were originally named (36) to designate the size of the region in kilobases and the tRNA identity (e.g., 8T is an 8-kb region that interrupts a tRNA that codes for a threonine). SARs are labeled by chromosome and region order within the chromosome (e.g., SAR 1-8 is the eighth shared anomalous region on chromosome 1).…”

Section: ϫ5mentioning

confidence: 99%

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Analysis of TenBrucellaGenomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle

et al. 2009

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The facultative intracellular bacterial pathogen Brucella infects a wide range of warm-blooded land and marine vertebrates and causes brucellosis. Currently, there are nine recognized Brucella species based on host preferences and phenotypic differences. The availability of 10 different genomes consisting of two chromosomes and representing six of the species allowed for a detailed comparison among themselves and relatives in the order Rhizobiales. Phylogenomic analysis of ortholog families shows limited divergence but distinct radiations, producing four clades as follows: Brucella abortus-Brucella melitensis, Brucella suis-Brucella canis, Brucella ovis, and Brucella ceti. In addition, Brucella phylogeny does not appear to reflect the phylogeny of Brucella species' preferred hosts. About 4.6% of protein-coding genes seem to be pseudogenes, which is a relatively large fraction. Only B. suis 1330 appears to have an intact ␤-ketoadipate pathway, responsible for utilization of plant-derived compounds. In contrast, this pathway in the other species is highly pseudogenized and consistent with the "domino theory" of gene death. There are distinct shared anomalous regions (SARs) found in both chromosomes as the result of horizontal gene transfer unique to Brucella and not shared with its closest relative Ochrobactrum, a soil bacterium, suggesting their acquisition occurred in spite of a predominantly intracellular lifestyle. In particular, SAR 2-5 appears to have been acquired by Brucella after it became intracellular. The SARs contain many genes, including those involved in O-polysaccharide synthesis and type IV secretion, which if mutated or absent significantly affect the ability of Brucella to survive intracellularly in the infected host.Brucellosis is a disease caused by bacteria of the genus Brucella. This disease is zoonotic and endemic in many areas throughout the world, causing chronic infections with common outcomes being abortion and sterility in infected animals. In humans, it is a severe acute febrile disease, producing focal lesions in bones, joints, the genitourinary tract, and other organs. Complications may include arthritis, sacroiliitis, spondylitis, and central nervous system effects. Brucella can cause abortions in women (as can other bacteria), mostly in the first and second trimesters of pregnancy (21, 27), and men can exhibit epididymo-orchitis (37).Currently, there are nine recognized species of Brucella, based on host preferences and phenotypic differences. Six classically recognized species are Brucella abortus (cattle), Brucella canis (dogs), Brucella melitensis (sheep and goats), Brucella neotomae (desert wood rats), Brucella ovis (sheep), and Brucella suis (pigs, reindeer, and hares). These six species have been subdivided into 18 biovars based on a panel of culture and biochemical characteristics (41). Recently, three additional species have been identified, namely Brucella microti from voles (49), "Brucella pinnipediae" from pinnipeds, and Brucella ceti from cetaceans (20).The genome from...

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Section: Resultsmentioning

confidence: 68%

Section: ϫ5mentioning

confidence: 99%

Analysis of TenBrucellaGenomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle

et al. 2009

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“…The genomic location of six GIs in P. aeruginosa was identical to those in our previous report [18], but their mobility was not determined. A number of studies have also described the regions of GIs in these four strains [14,[19][20][21][22][23]. These data have been presented in comparison with the 11 GIs of the present study ( Table 4).…”

Section: Discussionmentioning

confidence: 55%

“…These data have been presented in comparison with the 11 GIs of the present study ( Table 4). The Islander program can determine the GIs that possess tRNA/tmRNA-type flanking sequence and tyrosine-type integrases [19]. However, we obtained more mobile GIs than ones identified by Islander.…”

Section: Discussionmentioning

confidence: 84%

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Song

Zhang

2011

Chin. Sci. Bull.

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Mobile genomic islands (GIs) can be excised from the chromosome, then form a circular intermediate and be reintegrated into the chromosome by the GI internal integrase. Some mobile GIs can also be transferred into a new receptor cell by transformation, conjugation, or transduction. The action sites of the integrase are usually flanked direct repeats (DRs) of the GIs. Accurate localization of the flanking sequences is a precondition for determining the mobility of the GI. Mobile GIs are generally associated with transfer RNAs (tRNAs). Based on the correlation between flanking sequences and tRNA sequences, the flanking sequences of 11 putative mobile GIs in Pseudomonas aeruginosa PAO1, P. aeruginosa PA14, P. fluorescens Pf-5 and P. fluorescens Pf0-1 were identified. Among the 11 GIs, Pf0-1GI-1 is responsible for benzoate degradation. PAO1GI-1, Pf5GI-2, Pf5GI-3, and Pf5GI-4 were confirmed experimentally to be excised from a chromosome to form a circular intermediate. The action sites of the integrases are these GIs direct repeats. Due to distinct DRs, cutting sites for the internal integrase of PAO1GI-1, Pf5GI-2, Pf5GI-3 and Pf5GI-4 were determined outside the T-loop of the tRNA Gly gene, outside the anticodon loop of the tRNA Ser gene and tRNALys gene, and at the asymmetric 3′-end of the tRNA Leu gene, respectively. PAO1GI-1 and other mobile GIs may be transferred into many different strains that belong to different phyla because of the clear flanking sequences. This study describes basic information about the action sites of the integrases, assesses the mobility of GIs, and can help design and transfer mobile GIs to candidate strains. Pseudomonas, genomic islands, accurate localization, excision, integraseCitation: Song L, Zhang X H. Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens.

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“…For example Islander (Mantri and Williams 2004) and IslandPath (Hsiao et al 2003), two Web-based suites, combine and overlap several GI-related features trying to predict genomic regions as close as possible to the GI structural definition.…”

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confidence: 99%

Resolving the structural features of genomic islands: A machine learning approach

Vernikos¹,

Parkhill²

2007

Genome Res.

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Large inserts of horizontally acquired DNA that contain functionally related genes with limited phylogenetic distribution are often referred to as genomic islands (GIs), and structural definitions of these islands, based on common features, have been proposed. Although a large number of mobile elements fall well within the GI definition, there are several concerns about the structural consensus for GIs: The current GI definition was put forward 10 yr ago when only 12 complete bacterial genomes were available, a large number of GIs deviate from that definition, and in silico predictions assuming a full/partial GI structural model bias the sampling of the GI structural space toward "well-structured" GIs. In this study, the structural features of genomic regions are sampled by a hypothesis-free, bottom-up search, and these are exploited in a machine learning approach with the aim of explicitly quantifying and modeling the contribution of each feature to the GI structure. Performing a whole-genome-based comparative analysis between 37 strains of three different genera and 12 outgroup genomes, 668 genomic regions were sampled and used to train structural GI models. The data show that, overall, GIs from the three different genera fall into distinct, genus-specific structural families. However, decreasing the taxa resolution, by studying GI structures across different genus boundaries, provides models that converge on a fairly similar GI structure, further suggesting that GIs can be seen as a superfamily of mobile elements, with core and variable structural features, rather than a well-defined family.

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Islander: a database of integrative islands in prokaryotic genomes, the associated integrases and their DNA site specificities

Cited by 102 publications

References 20 publications

Analysis of TenBrucellaGenomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle

Analysis of TenBrucellaGenomes Reveals Evidence for Horizontal Gene Transfer Despite a Preferred Intracellular Lifestyle

Accurate localization and excision of genomic islands in four strains of Pseudomonas aeruginosa and Pseudomonas fluorescens

Resolving the structural features of genomic islands: A machine learning approach

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