IS4 family goes genomic

Palmenaer, Daniel De; Siguier, Patricia; Mahillon, Jacques

doi:10.1186/1471-2148-8-18

Cited by 57 publications

(55 citation statements)

References 72 publications

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“…In contrast to many hypervariable genomic islands (18,52,94), the MC-1 putative MAI contains no transposon genes within the island, and thus the position of the MAI within the genome is likely to be more stable than those in other MTB. However, some characteristic features of genomic islands are in close proximity to the island; for example, two genes with homology to insertion sequence elements of the IS4 family (35) and three tRNA genes that often serve as attachment sites for phages are located upstream of the MAI. In addition, 14 prophages were identified distributed throughout the genome.…”

Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1

Schübbe

Williams

Xie

et al. 2009

Appl Environ Microbiol

101

116

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The marine bacterium strain MC-1 is a member of the alpha subgroup of the proteobacteria that contains the magnetotactic cocci and was the first member of this group to be cultured axenically. The magnetotactic cocci are not closely related to any other known alphaproteobacteria and are only distantly related to other magnetotactic bacteria. The genome of MC-1 contains an extensive (102 kb) magnetosome island that includes numerous genes that are conserved among all known magnetotactic bacteria, as well as some genes that are unique. Interestingly, certain genes that encode proteins considered to be important in magnetosome assembly (mamJ and mamW) are absent from the genome of MC-1. Magnetotactic cocci exhibit polar magneto-aerotaxis, and the MC-1 genome contains a relatively large number of identified chemotaxis genes. Although MC-1 is capable of both autotrophic and heterotrophic growth, it does not appear to be metabolically versatile, with heterotrophic growth confined to the utilization of acetate. Central carbon metabolism is encoded by genes for the citric acid cycle (oxidative and reductive), glycolysis, and gluconeogenesis. The genome also reveals the presence or absence of specific genes involved in the nitrogen, sulfur, iron, and phosphate metabolism of MC-1, allowing us to infer the presence or absence of specific biochemical pathways in strain MC-1. The pathways inferred from the MC-1 genome provide important information regarding central metabolism in this strain that could provide insights useful for the isolation and cultivation of new magnetotactic bacterial strains, in particular strains of other magnetotactic cocci.Almost all magnetotactic bacteria (MTB) are microaerophiles that are most abundant at the oxic-anoxic interface (OAI) of natural aquatic environments, where magnetotactic cocci are often ubiquitous and the most dominant morphotype of MTB (43). The original discovery of MTB was based on the observation of polar magnetotaxis (44) in the magnetotactic cocci (19). In addition, phylogenetic studies of the magnetotactic cocci revealed a surprising degree of diversity (104, 105) in spite of their virtually identical cell morphology of coccoid to ovoid cells that are bilophotrichously flagellated on one side of the cell (27,45,71). These organisms are phylogenetically distinct from other MTB and form a clade at the base of the alphaproteobacterial branch on the tree of life, whereas other MTB of the Alphaproteobacteria (e.g., Magnetospirillum) are nested deep within the group (106). Despite their ubiquity in natural aquatic systems, for many years only one strain of magnetotactic cocci, designated strain MC-1, was isolated and grown in pure culture (44). Recently, another related strain was isolated, but it has not yet been characterized by molecular taxonomy (70). Strain MC-1 is a marine species that was isolated from water collected from the OAI of the Pettaquamscutt Estuary (Narragansett, RI) (34). It is presently in the process of valid description as "Magnetococcus marinus."Cells of s...

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Section: Resultsmentioning

confidence: 99%

Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1

Schübbe

Williams

Xie

et al. 2009

Appl Environ Microbiol

101

116

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“…They generate 5 bp to 6 bp AT-rich DR and are present in both Archaea and bacteria (150). Certain members generate very long variable DR (e.g., IS1634 from 17 to 478 bp, (154); ISCsa8 from 16 to 131 bp; ISMhp1, 80 bp).…”

Section: Is1634mentioning

confidence: 99%

“…The accumulation of additional related IS has permitted a more detailed analysis of the IS4 family, which had already become heterogeneous displaying extremely elevated levels of internal divergence (150). Based on more than 200 IS4-related sequences from bacterial and archaeal genome sequences, seven subgroups and three emerging families (IS701, ISH3, and IS1634) were defined.…”

Section: The Redefined Is4 and Related Familiesmentioning

confidence: 99%

Everyman's Guide to Bacterial Insertion Sequences

et al. 2015

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The number and diversity of known prokaryotic insertion sequences (IS) have increased enormously since their discovery in the late 1960s. At present the sequences of more than 4000 different IS have been deposited in the specialized ISfinder database. Over time it has become increasingly apparent that they are important actors in the evolution of their host genomes and are involved in sequestering, transmitting, mutating and activating genes, and in the rearrangement of both plasmids and chromosomes. This review presents an overview of our current understanding of these transposable elements (TE), their organization and their transposition mechanism as well as their distribution and genomic impact. In spite of their diversity, they share only a very limited number of transposition mechanisms which we outline here. Prokaryotic IS are but one example of a variety of diverse TE which are being revealed due to the advent of extensive genome sequencing projects. A major conclusion from sequence comparisons of various TE is that frontiers between the different types are becoming less clear. We detail these receding frontiers between different IS-related TE. Several, more specialized chapters in this volume include additional detailed information concerning a number of these.In a second section of the review, we provide a detailed description of the expanding variety of IS, which we have divided into families for convenience. Our perception of these families continues to evolve and families emerge regularly as more IS are identified. This section is designed as an aid and a source of information for consultation by interested specialist readers.

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“…Individual IS elements can be grouped into IS families based on characteristics such as transposase homology, transposase motifs, terminal inverted repeat (TIR) length, and composition, target specificity, and direct repeat (DR) length (6,13). The majority of IS elements are flanked by DR sequences that arise from staggered DNA cuts at the target site, followed by pasting of the IS elements into the insertion locus.…”

mentioning

confidence: 99%

Acinetobacter Insertion Sequence IS Aba11 Belongs to a Novel Family That Encodes Transposases with a Signature HHEK Motif

Rieck¹,

Tourigny²,

Crosatti³

et al. 2012

Appl Environ Microbiol

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Experimental and in silico PCR analysis targeting ISAba11 and TnAbaR islands in 196 epidemiologically unrelatedAcinetobacter strains representative of >19 species were performed. The first two Acinetobacter baumannii ISAba11 elements identified had been found to map to the same site on TnAbaR transposons. However, no further evidence of physical linkage between the two elements was demonstrated. Indeed, examination of 25 definite or putative insertion sites suggested limited sequence specificity. Importantly, an aacC1-tagged version of ISAba11 was shown to actively transpose in A. baumannii. Similarity searches identified nine iso-ISAba11 elements in Acinetobacter and one in Enhydrobacter and single representatives of four distant homologs in bacteria belonging to the phyla "Cyanobacteria" and Proteobacteria. Phylogenetic, sequence, and structural analyses of ISAba11 and/or its associated transposase (Tnp ISAba11 ) suggested that these elements be assigned to a new family. All five homologs encode transposases with a shared extended signature comprising 16 invariant residues within the N2, N3, and C1 regions, four of which constituted the cardinal ISAba11 family HHEK motif that is substituted for the YREK DNA binding motif conserved in the IS4 family. Additionally, ISAba11 family members were associated with either no flanking direct repeat (DR) or an ISAba11-typical 5-bp DR and possessed variable-length terminal inverted repeats that exhibited extensive intrafamily sequence identity. Given the limited pairwise identity among Tnp ISAba11 homologs and the observed restricted distribution of ISAba11, we propose that substantial gaps persist in the evolutionary record of ISAba11 and that this element represents a recent though potentially highly significant entrant into the A. baumannii gene pool.

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IS4 family goes genomic

Cited by 57 publications

References 72 publications

Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1

Complete Genome Sequence of the Chemolithoautotrophic Marine Magnetotactic Coccus Strain MC-1

Everyman's Guide to Bacterial Insertion Sequences

Acinetobacter Insertion Sequence IS Aba11 Belongs to a Novel Family That Encodes Transposases with a Signature HHEK Motif

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