Insertion sequence evolutionary patterns highlight convergent genetic inactivations and recent genomic island acquisitions among epidemic Burkholderia cenocepacia

ABSTRACTSalmonellagenomic island 1 (SGI1) is a 43-kb integrative mobilizable element that harbors a great diversity of multidrug resistance gene clusters described in numerousSalmonella entericaserovars and also inProteus mirabilis. The majority of SGI1 variants contain an In104-derivative complex class 1 integron inserted between resolvase generesand open reading frame (ORF) S044 in SGI1. Recently, the international spread of ciprofloxacin-resistantS. entericaserovar Kentucky sequence type 198 (ST198) containing SGI1-K variants has been reported. A retrospective study was undertaken to characterize ST198S. Kentucky strains isolated before the spread of the epidemic ST198-SGI1-K population in Africa and the Middle East. Here, we characterized 12 ST198S. Kentucky strains isolated between 1969 and 1999, mainly from humans returning from Southeast Asia (n= 10 strains) or Israel (n= 1 strain) or from meat in Egypt (n= 1 strain). All these ST198S. Kentucky strains did not belong to the XbaI pulsotype X1 associated with the African epidemic clone but to pulsotype X2. SGI1-J subgroup variants containing different complex integrons with a partial transposition module and inserted within ORF S023 of SGI1 were detected in six strains. The SGI1-J4 variant containing a partially deleted class 1 integron and thus showing a narrow resistance phenotype to sulfonamides was identified in two epidemiologically unrelated strains from Indonesia. The four remaining strains harbored a novel SGI1-J variant, named SGI1-J6, which containedaadA2,floR2,tetR(G)-tetA(G), andsul1resistance genes within its complex integron. Moreover, in all theseS. Kentucky isolates, a novel insertion sequence related to the IS630family and named ISSen5was found inserted upstream of the SGI1 complex integron in ORF S023. Thus, two subpopulations ofS. Kentucky ST198 independently and exclusively acquired the SGI1 during the 1980s and 1990s. Unlike the ST198-X1 African epidemic subpopulation, the ST198-X2 subpopulation mainly from Asia harbors variants of the SGI1-J subgroup that are encountered mainly in the Far East, as previously described forS. entericaserovars Emek and Virchow.

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CRISPR-based screening of genomic island excision events in bacteria

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1508525112 ◽

2015 ◽

Vol 112 (26) ◽

pp. 8076-8081 ◽

Cited By ~ 76

Author(s):

Kurt Selle ◽

Todd R. Klaenhammer ◽

Rodolphe Barrangou

Keyword(s):

Insertion Sequence ◽

Genomic Island ◽

Driving Forces ◽

Genomic Analysis ◽

Adaptive Immune System ◽

Population Level ◽

Streptococcus Thermophilus ◽

Genomic Islands ◽

Common Mechanism ◽

Sequence Elements

Genomic analysis ofStreptococcus thermophilusrevealed that mobile genetic elements (MGEs) likely contributed to gene acquisition and loss during evolutionary adaptation to milk. Clustered regularly interspaced short palindromic repeats–CRISPR-associated genes (CRISPR-Cas), the adaptive immune system in bacteria, limits genetic diversity by targeting MGEs including bacteriophages, transposons, and plasmids. CRISPR-Cas systems are widespread in streptococci, suggesting that the interplay between CRISPR-Cas systems and MGEs is one of the driving forces governing genome homeostasis in this genus. To investigate the genetic outcomes resulting from CRISPR-Cas targeting of integrated MGEs,in silicoprediction revealed four genomic islands without essential genes in lengths from 8 to 102 kbp, totaling 7% of the genome. In this study, the endogenous CRISPR3 type II system was programmed to target the four islands independently through plasmid-based expression of engineered CRISPR arrays. TargetinglacZwithin the largest 102-kbp genomic island was lethal to wild-type cells and resulted in a reduction of up to 2.5-log in the surviving population. Genotyping of Lac−survivors revealed variable deletion events between the flanking insertion-sequence elements, all resulting in elimination of the Lac-encoding island. Chimeric insertion sequence footprints were observed at the deletion junctions after targeting all of the four genomic islands, suggesting a common mechanism of deletion via recombination between flanking insertion sequences. These results established that self-targeting CRISPR-Cas systems may direct significant evolution of bacterial genomes on a population level, influencing genome homeostasis and remodeling.

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Genomics Reveals a Unique Clone of Burkholderia cenocepacia Harboring an Actively Excising Novel Genomic Island

Frontiers in Microbiology ◽

10.3389/fmicb.2017.00590 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 5

Author(s):

Prashant P. Patil ◽

Swapna Mali ◽

Samriti Midha ◽

Vikas Gautam ◽

Lona Dash ◽

...

Keyword(s):

Genomic Island ◽

Burkholderia Cenocepacia ◽

Unique Clone

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Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

BMC Genomics ◽

10.1186/s12864-020-07178-6 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Guislaine Refrégier ◽

Christophe Sola ◽

Christophe Guyeux

Keyword(s):

Mycobacterium Tuberculosis ◽

Insertion Sequence ◽

Recent Common Ancestor ◽

Direct Repeats ◽

Evolutionary Mechanisms ◽

Evolutionary Patterns ◽

Crispr Locus ◽

Most Recent Common Ancestor ◽

Low Diversity ◽

Set Up

Abstract Background Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes. Results We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs. We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110 insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110 insertions or between Direct Repeats. Conclusion This work definitively shows that CRISPR locus of M. tuberculosis did not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.

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The Burkholderia cepacia Epidemic Strain Marker Is Part of a Novel Genomic Island Encoding Both Virulence and Metabolism-Associated Genes in Burkholderia cenocepacia

Infection and Immunity ◽

10.1128/iai.72.3.1537-1547.2004 ◽

2004 ◽

Vol 72 (3) ◽

pp. 1537-1547 ◽

Cited By ~ 108

Author(s):

Adam Baldwin ◽

Pamela A. Sokol ◽

Julian Parkhill ◽

Eshwar Mahenthiralingam

Keyword(s):

Burkholderia Cepacia ◽

Genomic Island ◽

Fatty Acid Biosynthesis ◽

Random Amplified Polymorphic Dna ◽

Gc Content ◽

Transcriptional Regulator ◽

Homoserine Lactone ◽

Burkholderia Cenocepacia ◽

Epidemic Strain ◽

Isogenic Mutants

ABSTRACT The Burkholderia cepacia epidemic strain marker (BCESM) is a useful epidemiological marker for virulent B. cenocepacia strains that infect patients with cystic fibrosis. However, there was no evidence that the original marker, identified by random amplified polymorphic DNA fingerprinting, contributed to pathogenicity. Here we demonstrate that the BCESM is part of a novel genomic island encoding genes linked to both virulence and metabolism. The BCESM was present on a 31.7-kb low-GC-content island that encoded 35 predicted coding sequences (CDSs): an N-acyl homoserine lactone (AHL) synthase gene (cciI) and corresponding transcriptional regulator (cciR), representing the first time cell signaling genes have been found on a genomic island; fatty acid biosynthesis genes; an IS66 family transposase; transcriptional regulator CDSs; amino acid metabolism genes; and a group of hypothetical genes. Mutagenesis of the AHL synthase, amidase (amiI), and porin (opcI) genes on the island was carried out. Testing of the isogenic mutants in a rat model of chronic lung infection demonstrated that the amidase played a role in persistence, while the AHL synthase and porin were both involved in virulence. The island, designated the B. cenocepacia island (cci), is the first genomic island to be defined in the B. cepacia complex and its discovery validates the original epidemiological correlation of the BCESM with virulent CF strains. The features of the cci, which overlap both pathogenicity and metabolism, expand the concept of bacterial pathogenicity islands and illustrate the diversity of accessory functions that can be acquired by lateral gene transfer in bacteria.

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Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis

10.1101/2019.12.13.875765 ◽

2019 ◽

Author(s):

Guislaine Refrégier ◽

Christophe Sola ◽

Christophe Guyeux

Keyword(s):

Mycobacterium Tuberculosis ◽

Insertion Sequence ◽

Recent Common Ancestor ◽

Direct Repeats ◽

Evolutionary Mechanisms ◽

Evolutionary Patterns ◽

Crispr Locus ◽

Most Recent Common Ancestor ◽

Low Diversity ◽

Set Up

AbstractDiversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes.We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs.We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110 insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110 insertions or between Direct Repeats.This work definitively shows that CRISPR locus of M. tuberculosis did not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.

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Evolutionary patterns of the Ediacara biota

AccessScience ◽

10.1036/1097-8542.yb100137 ◽

2015 ◽

Keyword(s):

Evolutionary Patterns ◽

Ediacara Biota

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Evolutionary Patterns of Retinal-Binding Pockets of Type I Rhodopsins and Their Functions†

Photochemistry and Photobiology ◽

10.1562/2006-02-14-ra-802 ◽

2006 ◽

Vol 82 (6) ◽

pp. 1426 ◽

Cited By ~ 1

Author(s):

Larisa Adamian ◽

Zheng Ouyang ◽

Yan Yuan Tseng ◽

Jie Liang

Keyword(s):

Type I ◽

Evolutionary Patterns ◽

Binding Pockets

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Comparative Analysis of Genetic and Morphological Variation within the Platanthera hyperborea Complex (Orchidaceae)

Systematic Botany ◽

10.1600/036364420x16033962925303 ◽

2020 ◽

Vol 45 (4) ◽

pp. 767-778

Author(s):

Eranga Wettewa ◽

Nick Bailey ◽

Lisa E. Wallace

Keyword(s):

North America ◽

Diploid Species ◽

Morphological Characters ◽

Evolutionary Patterns ◽

Founding Population ◽

Multiple Origins ◽

Geographic Structure ◽

Species Complexes ◽

Nuclear Its ◽

Cryptic Taxa

Abstract—Species complexes present considerable problems for a working taxonomy due to the presence of intraspecific variation, hybridization, polyploidy, and phenotypic plasticity. Understanding evolutionary patterns using molecular markers can allow for a more thorough assessment of evolutionary lineages than traditional morphological markers. In this study, we evaluated genetic diversity and phylogenetic patterns among taxa of the Platanthera hyperborea (Orchidaceae) complex, which includes diploid (Platanthera aquilonis) and polyploid (Platanthera hyperborea, P. huronensis, and P. convallariifolia) taxa spanning North America, Greenland, Iceland, and Asia. We found that three floral morphological characters overlap among the polyploid taxa, but the diploid species has smaller flowers. DNA sequence variation in a plastid (rpL16 intron) and a nuclear (ITS) marker indicated that at least three diploid species have contributed to the genomes of the polyploid taxa, suggesting all are of allopolyploid origin. Platanthera convallariifolia is most like P. dilatata and P. stricta, whereas P. huronensis and P. hyperborea appear to have originated from crosses of P. dilatata and P. aquilonis. Platanthera huronensis, which is found across North America, has multiple origins and reciprocal maternal parentage from the diploid species. By contrast, P. hyperborea, restricted to Greenland and Iceland, appears to have originated from a small founding population of hybrids in which P. dilatata was the maternal parent. Geographic structure was found among polyploid forms in North America. The area of Manitoba, Canada appears to be a contact zone among geographically diverse forms from eastern and western North America. Given the geographic and genetic variation found, we recommend continued recognition of four green-flowered species within this complex, but caution that there may be additional cryptic taxa within North America.

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