scholarly journals Crucial Role for Insertion Sequence Elements in Lactobacillus helveticus Evolution as Revealed by Interstrain Genomic Comparison

2009 ◽  
Vol 76 (1) ◽  
pp. 212-220 ◽  
Author(s):  
Pawel Kaleta ◽  
John O'Callaghan ◽  
Gerald F. Fitzgerald ◽  
Thomas P. Beresford ◽  
R. Paul Ross
Keyword(s):  
Insertion Sequence ◽  
Bacterial Genome ◽  
Lactobacillus Helveticus ◽  
Open Reading Frames ◽  
Comparative Genome Hybridization ◽  
Genome Plasticity ◽  
Genomic Comparison ◽  
Is Elements ◽  
Accelerated Evolution ◽  
Sequence Elements

ABSTRACT Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence (IS) element expansion in association with massive gene decay. To assess this diversity and examine the level of genome plasticity within the L. helveticus species, an array-based comparative genome hybridization (aCGH) experiment was designed in which 10 strains were analyzed. The aCGH experiment revealed 16 clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered ISs were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63). These findings contribute to the overall viewpoint of the versatile character of IS elements and the role they may play in bacterial genome plasticity.

scholarly journals Characterization of the IS200/IS605 Insertion Sequence Family in Halanaerobium Hydrogeniformans

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 484
Author(s):  
Michael Sadler ◽  
Melanie R. Mormile ◽  
Ronald L. Frank
Keyword(s):  
Insertion Sequence ◽  
Open Reading Frames ◽  
Insertion Sequences ◽  
Genome Plasticity ◽  
Mobile Dna ◽  
Dna Elements ◽  
Left And Right ◽  
Evolutionary Role ◽  
Reading Frames

Mobile DNA elements play a significant evolutionary role by promoting genome plasticity. Insertion sequences are the smallest prokaryotic transposable elements. They are highly diverse elements, and the ability to accurately identify, annotate, and infer the full genomic impact of insertion sequences is lacking. Halanaerobium hydrogeniformans is a haloalkaliphilic bacterium with an abnormally high number of insertion sequences. One family, IS200/IS605, showed several interesting features distinct from other elements in this genome. Twenty-three loci harbor elements of this family in varying stages of decay, from nearly intact to an ends-only sequence. The loci were characterized with respect to two divergent open reading frames (ORF), tnpA and tnpB, and left and right ends of the elements. The tnpB ORF contains two nearly identical insert sequences that suggest recombination between tnpB ORF is occurring. From these results, insertion sequence activity can be inferred, including transposition capability and element interaction.

scholarly journals Easy identification of insertion sequence mobilization events in related bacterial strains with ISCompare

2021 ◽  
Author(s):  
Ezequiel G Mogro ◽  
Nicolás M Ambrosis ◽  
Mauricio J Lozano
Keyword(s):  
Insertion Sequence ◽  
Bacterial Genome ◽  
Draft Genome ◽  
Genome Plasticity ◽  
Bacterial Strains ◽  
Bacterial Genomes ◽  
A Genome ◽  
Phenotypic Variations ◽  
Genome Assemblies ◽  
Straightforward Approach

Abstract Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

scholarly journals Complete DNA Sequence of Yersinia enterocolitica Serotype 0:8 Low-Calcium-Response Plasmid Reveals a New Virulence Plasmid-Associated Replicon

2001 ◽  
Vol 69 (7) ◽  
pp. 4627-4638 ◽  
Author(s):  
Norma J. Snellings ◽  
Michael Popek ◽  
Luther E. Lindler
Keyword(s):  
Yersinia Enterocolitica ◽  
Insertion Sequence ◽  
Open Reading Frames ◽  
Virulence Plasmid ◽  
Calcium Response ◽  
Is Elements ◽  
New Genes ◽  
Low Calcium ◽  
Reading Frames ◽  
Plasmid Replicons

ABSTRACT The complete nucleotide sequence and organization of theYersinia enterocolitica serotype 0:8 low-calcium-response (LCR) plasmid, pYVe8081, were determined. The 67,720-bp plasmid encoded all the genes known to be part of the LCR stimulon except for ylpA. Eight of 13 intact open reading frames of unknown function identified in pYVe8081 had homologues in Yersinia pestis plasmid pCD1 or inY. enterocolitica serotype 0:9 plasmid pYVe227. A region of approximately 17 kbp showed no DNA identity to pCD1 or pYVe227 and contained six potential new genes, a possible new replicon, and two intact insertion sequence (IS) elements. One intact IS element, ISYen1, was a new IS belonging to the IS256 family. Several vestigial IS elements appeared different from the IS distribution seen in the other LCR plasmids. The RepA proteins encoded by Y. enterocoliticaserotype 0:8 pYVeWA and pYVe8081 were identical. The putative pYVe8081 replicon showed significant homology to the IncL/M replicon of pMU407.1 but was only distantly related to the replicons of pCD1 and pYVe227. In contrast, the putative partitioning genes of pYVe8081 showed 97% DNA identity to the spy/sopABC loci of pCD1 and pYVe227. Sequence analysis suggests thatYersinia LCR plasmids are from a common ancestor but that Y. enterocolitica serotype 0:8 plasmid replicons may have evolved independently via cointegrate formation following a transposition event. The change in replicon structure is predicted to change the incompatibility properties of Y. enterocolitica serotype 0:8 plasmids from those of Y. enterocolitica serotype 0:9 and Y. pestis LCR plasmids.

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 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 Genetic Diversity in the Lactose Operons of Lactobacillus helveticus Strains and Its Relationship to the Role of These Strains as Commercial Starter Cultures

2005 ◽  
Vol 71 (3) ◽  
pp. 1655-1658 ◽  
Author(s):  
M. J. Callanan ◽  
T. P. Beresford ◽  
R. P. Ross
Keyword(s):  
Genetic Diversity ◽  
Type Strain ◽  
Insertion Sequence ◽  
Starter Cultures ◽  
Lactobacillus Helveticus ◽  
Galactosidase Activity ◽  
Genes Encoding ◽  
Sequence Elements ◽  
Insertion Sequence Elements

ABSTRACT Two novel insertion sequence elements, ISLhe1 and ISLhe15, were located upstream of the genes encoding the β-galactosidase enzyme in Lactobacillus helveticus commercial starter strains. Strains with the IS982 family element, ISLhe1, demonstrated reduced β-galactosidase activity compared to the L. helveticus type strain, whereas strains with the ISLhe15 element expressed β-galactosidase in the absence of lactose.

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