Shuffling of Sulfolobus genomes by autonomous and non-autonomous mobile elements

2004 ◽  
Vol 32 (2) ◽  
pp. 179-183 ◽  
Author(s):  
K. Brügger ◽  
E. Torarinsson ◽  
P. Redder ◽  
L. Chen ◽  
R.A. Garrett
Keyword(s):  
Experimental Data ◽  
Insertion Sequence ◽  
Sulfolobus Solfataricus ◽  
Mobile Element ◽  
Mobile Elements ◽  
Sulfolobus Tokodaii ◽  
Is Elements ◽  
Large Numbers ◽  
Sequence Elements ◽  
Insertion Sequence Elements

Each of the sequenced Sulfolobus genomes contains large numbers of putatively mobile elements, both IS elements (insertion sequence elements) and MITEs (miniature inverted-repeat transposable elements). There are 344 in the 3.0 Mb genome of Sulfolobus solfataricus P2 and 95 in the 2.7 Mb genome of Sulfolobus tokodaii. In the former they constitute more than 10% of the genome. Experimental data suggest that transposition of IS elements occurs frequently. Moreover, the gene order between the two organisms differs greatly, indicating that multiple rearrangements have occurred. This has also led to considerable speculation as to how the cells are viable. Recently, a third Sulfolobus genome was completed which contains no IS elements or MITEs. This enabled us to compare the gene orders of the three genomes and provide evidence for mobile element-induced rearrangements of sections of the genomes.

scholarly journals Mutations and Rearrangements in the Genome of Sulfolobus solfataricus P2

2006 ◽  
Vol 188 (12) ◽  
pp. 4198-4206 ◽  
Author(s):  
Peter Redder ◽  
Roger A. Garrett
Keyword(s):  
Sulfolobus Solfataricus ◽  
Mobile Element ◽  
Progressive Increase ◽  
Mobile Elements ◽  
Is Elements ◽  
Copy Numbers ◽  
Different Types ◽  
Single Deletion ◽  
Insight Into

ABSTRACT The genome of Sulfolobus solfataricus P2 carries a larger number of transposable elements than any other sequenced genome from an archaeon or bacterium and, as a consequence, may be particularly susceptible to rearrangement and change. In order to gain more insight into the natures and frequencies of different types of mutation and possible rearrangements that can occur in the genome, the pyrEF locus was examined for mutations that were isolated after selection with 5-fluoroorotic acid. About two-thirds of the 130 mutations resulted from insertions of mobile elements, including insertion sequence (IS) elements and a single nonautonomous mobile element, SM2. For each of these, the element was identified and shown to be present at its original genomic position, consistent with a progressive increase in the copy numbers of the mobile elements. In addition, several base pair substitutions, as well as small deletions, insertions, and a duplication, were observed, and about one-fifth of the mutations occurred elsewhere in the genome, possibly in an orotate transporter gene. One mutant exhibited a 5-kb genomic rearrangement at the pyrEF locus involving a two-step IS element-dependent reaction, and its boundaries were defined using a specially developed “in vitro library” strategy. Moreover, while searching for the donor mobile elements, evidence was found for two major changes that had occurred in the genome of strain P2, one constituting a single deletion of about 4% of the total genome (124 kb), while the other involved the inversion of a 25-kb region. Both were bordered by IS elements and were inferred to have arisen through recombination events. The results underline the caution required in working experimentally with an organism such as S. solfataricus with a continually changing genome.

scholarly journals TheSinorhizobium melilotiinsertion sequence (IS) elements ISRm102F34-1/ISRm7and ISRm220-13-5belong to a new family of insertion sequence elements

1999 ◽  
Vol 172 (1) ◽  
pp. 1-7 ◽  
Author(s):  
Werner Selbitschka ◽  
Sanae Zekri ◽  
Gerald Schröder ◽  
Alfred Pühler ◽  
Nicolás Toro
Keyword(s):  
Insertion Sequence ◽  
Is Elements ◽  
New Family ◽  
Sequence Elements ◽  
Insertion Sequence Elements

scholarly journals digIS: towards detecting distant and putative novel insertion sequence elements in prokaryotic genomes

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Janka Puterová ◽  
Tomáš Martínek
Keyword(s):  
Hidden Markov Models ◽  
Insertion Sequence ◽  
Markov Models ◽  
Hidden Markov ◽  
Software Tool ◽  
Is Elements ◽  
Profile Hidden Markov Models ◽  
Prokaryotic Genomes ◽  
Sequence Elements ◽  
Insertion Sequence Elements

Abstract Background The insertion sequence elements (IS elements) represent the smallest and the most abundant mobile elements in prokaryotic genomes. It has been shown that they play a significant role in genome organization and evolution. To better understand their function in the host genome, it is desirable to have an effective detection and annotation tool. This need becomes even more crucial when considering rapid-growing genomic and metagenomic data. The existing tools for IS elements detection and annotation are usually based on comparing sequence similarity with a database of known IS families. Thus, they have limited ability to discover distant and putative novel IS elements. Results In this paper, we present digIS, a software tool based on profile hidden Markov models assembled from catalytic domains of transposases. It shows a very good performance in detecting known IS elements when tested on datasets with manually curated annotation. The main contribution of digIS is in its ability to detect distant and putative novel IS elements while maintaining a moderate level of false positives. In this category it outperforms existing tools, especially when tested on large datasets of archaeal and bacterial genomes. Conclusion We provide digIS, a software tool using a novel approach based on manually curated profile hidden Markov models, which is able to detect distant and putative novel IS elements. Although digIS can find known IS elements as well, we expect it to be used primarily by scientists interested in finding novel IS elements. The tool is available at https://github.com/janka2012/digIS.

scholarly journals Novel Insertion Sequence Elements Associated with Genetic Heterogeneity and Phenotype Conversion in Ralstonia solanacearum

2000 ◽  
Vol 182 (16) ◽  
pp. 4673-4676 ◽  
Author(s):  
Eun-Lee Jeong ◽  
Jeremy N. Timmis
Keyword(s):  
Genetic Heterogeneity ◽  
Ralstonia Solanacearum ◽  
Insertion Sequence ◽  
Southern Hybridization ◽  
Insertion Sequences ◽  
Is Elements ◽  
Conversion Event ◽  
Sequence Elements ◽  
Different Strains ◽  
Insertion Sequence Elements

ABSTRACT Three insertion sequences (IS) elements were isolated from the phytopathogen Ralstonia solanacearum. Southern hybridization using these IS elements as probes revealed hybridization profiles that varied greatly between different strains of the pathogen. During a spontaneous phenotype conversion event, the promoter of thephcA gene was interrupted by one of these IS elements.

scholarly journals The Genome Sequence of Avibacterium paragallinarum Strain CL Has a Large Repertoire of Insertion Sequence Elements

2017 ◽  
Vol 5 (15) ◽  
Author(s):  
Guillermo Horta-Valerdi ◽  
Maria Patricia Sanchez-Alonso ◽  
Victor M. Perez-Marquez ◽  
Erasmo Negrete-Abascal ◽  
Sergio Vaca-Pacheco ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Insertion Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Content Type ◽  
Is Elements ◽  
Avibacterium Paragallinarum ◽  
Sequence Elements ◽  
Large Repertoire ◽  
Insertion Sequence Elements

ABSTRACT The draft genome sequence of Avibacterium paragallinarum strain CL serovar C is reported here. The genome comprises 154 contigs corresponding to 2.4 Mb with 41% G+C content and many insertion sequence (IS) elements, a characteristic not previously reported in A. paragallinarum.

scholarly journals Identification and characterization of Fep15, a new selenocysteine-containing member of the Sep15 protein family

2006 ◽  
Vol 394 (3) ◽  
pp. 575-579 ◽  
Author(s):  
Sergey V. Novoselov ◽  
Deame Hua ◽  
Alexey V. Lobanov ◽  
Vadim N. Gladyshev
Keyword(s):  
Mammalian Cells ◽  
Insertion Sequence ◽  
Phylogenetic Analyses ◽  
Dependent Manner ◽  
Putative Active Site ◽  
A Genome ◽  
Sequence Elements ◽  
Identification And Characterization ◽  
Insertion Sequence Elements

Sec (selenocysteine) is a rare amino acid in proteins. It is co-translationally inserted into proteins at UGA codons with the help of SECIS (Sec insertion sequence) elements. A full set of selenoproteins within a genome, known as the selenoproteome, is highly variable in different organisms. However, most of the known eukaryotic selenoproteins are represented in the mammalian selenoproteome. In addition, many of these selenoproteins have cysteine orthologues. Here, we describe a new selenoprotein, designated Fep15, which is distantly related to members of the 15 kDa selenoprotein (Sep15) family. Fep15 is absent in mammals, can be detected only in fish and is present in these organisms only in the selenoprotein form. In contrast with other members of the Sep15 family, which contain a putative active site composed of Sec and cysteine, Fep15 has only Sec. When transiently expressed in mammalian cells, Fep15 incorporated Sec in an SECIS- and SBP2 (SECIS-binding protein 2)-dependent manner and was targeted to the endoplasmic reticulum by its N-terminal signal peptide. Phylogenetic analyses of Sep15 family members suggest that Fep15 evolved by gene duplication.

scholarly journals Dynamics of Genome Architecture in Rhizobium sp. Strain NGR234

2002 ◽  
Vol 184 (1) ◽  
pp. 171-176 ◽  
Author(s):  
Patrick Mavingui ◽  
Margarita Flores ◽  
Xianwu Guo ◽  
Guillermo Dávila ◽  
Xavier Perret ◽  
...  
Keyword(s):  
Large Scale ◽  
Insertion Sequence ◽  
Biological Significance ◽  
Genome Architecture ◽  
Bacterial Genomes ◽  
Symbiotic Plasmid ◽  
Sequence Elements ◽  
Dynamic Structures ◽  
Genome Analyses ◽  
Insertion Sequence Elements

ABSTRACT Bacterial genomes are usually partitioned in several replicons, which are dynamic structures prone to mutation and genomic rearrangements, thus contributing to genome evolution. Nevertheless, much remains to be learned about the origins and dynamics of the formation of bacterial alternative genomic states and their possible biological consequences. To address these issues, we have studied the dynamics of the genome architecture in Rhizobium sp. strain NGR234 and analyzed its biological significance. NGR234 genome consists of three replicons: the symbiotic plasmid pNGR234a (536,165 bp), the megaplasmid pNGR234b (>2,000 kb), and the chromosome (>3,700 kb). Here we report that genome analyses of cell siblings showed the occurrence of large-scale DNA rearrangements consisting of cointegrations and excisions between the three replicons. As a result, four new genomic architectures have emerged. Three consisted of the cointegrates between two replicons: chromosome-pNGR234a, chromosome-pNGR234b, and pNGR234a-pNGR234b. The other consisted of a cointegrate of the three replicons (chromosome-pNGR234a-pNGR234b). Cointegration and excision of pNGR234a with either the chromosome or pNGR234b were studied and found to proceed via a Campbell-type mechanism, mediated by insertion sequence elements. We provide evidence showing that changes in the genome architecture did not alter the growth and symbiotic proficiency of Rhizobium derivatives.

Two identical nonylphenol monooxygenase genes linked to IS6100 and some putative insertion sequence elements in Sphingomonas sp. NP5

Microbiology ◽  
2012 ◽  
Vol 158 (7) ◽  
pp. 1796-1807 ◽  
Author(s):  
Masahiro Takeo ◽  
Yoshihiro Maeda ◽  
Junko Maeda ◽  
Naoki Nishiyama ◽  
Chitoshi Kitamura ◽  
...  
Keyword(s):  
Insertion Sequence ◽  
Sequence Elements ◽  
Insertion Sequence Elements
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